R/data.R
In molepi/DNAmArray: Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach
# TSV file with hg19 mask information for EPIC probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 865918 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
"EPIC.hg19.manifest.txt"
# TSV file with hg38 mask information for EPIC probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 865918 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# TSV file with hg19 mask information for 450K probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 485577 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# TSV file with hg38 mask information for 450K probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 485577 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# Data frame with coefficients for estimating blood counts
#
# Contains coefficients derived from the WBCC predictor
#
# @format A data frame with 481392 rows and 5 variables:
# \describe{
# \item{baso_perc}{coefficient for estimating basophils}
# \item{eos_perc}{coefficient for estimating eosinophils}
# \item{lymph_perc}{coefficient for estimating lymphocytes}
# \item{mono_perc}{coefficient for estimating monocytes}
# \item{neut_perc}{coefficient for estimating neutrophils}
#
# @usage data(DNAmPredictorCoef)
#
NULL
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# TSV file with hg19 mask information for EPIC probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 865918 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
"EPIC.hg19.manifest.txt"
# TSV file with hg38 mask information for EPIC probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 865918 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# TSV file with hg19 mask information for 450K probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 485577 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# TSV file with hg38 mask information for 450K probes
#
# Table containing all SNPs and short INDELS that overlap with
# EPIC probes.For each overlap there is an unique row. Consequently,
# some probes are duplicated (probes that overlap with multiple
# variants) and some variants are duplicated (some variants overlap
# with more than one probe).
#
#
# @format A data frame with 485577 rows and 57 variables:
# \describe{
# \item{CpG_chrm}{chromosome location of the target}
# \item{CpG_beg}{0-based co-ordinate of the target. The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{CpG_end}{1-based co-ordinate of the target.The
# co-ordinates should have a span of 2 nucleotides for
# CpG probes, or 1 nucleotide for CpH and SNP probes. Some
# erroneous CpH probe co-ordinates mapping information in
# the manufacturer's manifest have been corrected.}
# \item{probe_strand}{strand orientation of the actual
# probe. '+' is for all the up-probes positioned in
# smaller co-ordinates and '-' for all the down-probes
# positioned in greater co-ordinates with respect to
# the target CpGs. '*' is used for unmapped probes.}
# \item{probeID}{probe ID}
# \item{address_A}{address of probe A on the chip
# designated by the original manifest}
# \item{address_B}{address of probe B on the chip
# designated by the original manifest}
# \item{channel}{'Both' for type II probes and 'Grn' or
# 'Red' for Type I probes}
# \item{designType}{Type of probe, either 'I' or 'II'}
# \item{nextBase}{the actual extension base (on the probe
# strand) after bisulfite conversion ('A' or 'C' or 'T').
# Unmapped probes have extension base labeled in the original
# manifest.}
# \item{nextBaseRef}{the extension base (on the hybridized /
# template DNA) before bisulfite conversion ('A', 'C', 'G',
# or 'T'). Unmapped probes have 'NA'.}
# \item{probeType}{either 'cg', 'ch', or 'rs'}
# \item{orientation}{either 'up or 'down', specifying
# whether the probe is positioned upstream (in smaller
# co-ordinates) or downstream (in greater co-ordinates)
# from the target}
# \item{probeCpGcnt}{the number of additional CpGs in the
# probe (not counting the interrogated CpG)}
# \item{context35}{the number of CpGs in the [-35bp, +35bp]
# window}
# \item{probeBeg}{the mapped start position of the probe,
# which is always 50bp long}
# \item{probeEnd}{the mapped end position of the probe,
# which is always 50bp long}
# \item{ProbeSeq_A}{the probe sequence for allele A}
# \item{ProbeSeq_B}{the probe sequence for allele B}
# \item{gene}{comma separated list of gene annotations
# (unique and alphabetically sorted). Gene models follow
# GENCODE version 22 (hg38)}
# \item{gene_HGNC}{comma separated list of gene annotations
# (unique and alphabetically sorted). Genes are checked
# using HGNChelper for compatibility with HGNC. Gene models
# follows GENCODE version 22 (hg38)}
# \item{chrm_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{beg_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{flag_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{mapQ_A}{the mapping quality score for probe A excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{NM_A}{the mapping info for probe A excluding
# decoy chromosomes}
# \item{chrm_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{beg_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{flag_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{mapQ_B}{the mapping quality score for probe B excluding
# decoy chromosomes, with 60 being the best}
# \item{cigar_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{NM_B}{the mapping info for probe B excluding
# decoy chromosomes}
# \item{wDecoy_chrm_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_beg_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_flag_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_mapQ_A}{the mapping quality score for probe A including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_NM_A}{the mapping info for probe A including
# decoy chromosomes}
# \item{wDecoy_chrm_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_beg_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_flag_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_mapQ_B}{the mapping quality score for probe B including
# decoy chromosomes, with 60 being the best}
# \item{wDecoy_cigar_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{wDecoy_NM_B}{the mapping info for probe B including
# decoy chromosomes}
# \item{posMatch}{whether the mapping matches the original
# manifest, it only applies to hg19 and will be NA under
# hg38}
# \item{MASK_mapping}{whether the probe is masked for mapping
# reasons. Probes retained should have high quality (>=40)
# consistent (with designed MAPINFO) mapping (for both in the
# cast of type I) without INDELS}
# \item{MASK_typeINextBaseSwitch}{whether the probe has a SNP
# in the extension base that causes a color channel switch from
# the official annotation (described as color channel switching
# or CCS SNP in the reference). These probes should be processed
# differently than designed (by summin up both color channels
# instead of just the annotated color channel)}
# \item{MASK_rmsk15}{whetehr the 15bp 3'-subsequence of the
# probe overlaps with repeat masker, this MASK is NOT
# recommended}
# \item{MASK_sub40_copy}{whether the 40bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub35_copy}{whether the 35bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub30_copy}{whether the 30bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_sub25_copy}{whether the 25bp 3'subsequence of the
# probe is non-unique}
# \item{MASK_snp5_common}{whether 5bp 3'-subsequence (including
# extension for tyep II) overlaps with any of the common SNPs
# from dbSNP (global MAF can be under 1%)}
# \item{MASK_snp5_GMAF1p}{whether 5bp 3'-subsequence (including
# extension for type II) overlaps with any of the SNPs with
# global MAF > 1%}
# \item{MASK_extBase}{probes masked for extension base inconsistent
# with specified color channel (type I) or CpG (Type II) based
# on mapping}
# \item{MASK_general}{recommended general ppurpose masking
# merged from MASK_sub30_copy, MASK_mapping, MASK_extBase,
# MASK_typeINExtBaseSwitch and MASK_snp5_GMAF1p}
#
# @usage read_tsv('data/EPIC.hg19.manifest.tsv.gz')
#
# @source
# \url{http://zwdzwd.github.io/InfiniumAnnotation}
#
NULL
# Data frame with coefficients for estimating blood counts
#
# Contains coefficients derived from the WBCC predictor
#
# @format A data frame with 481392 rows and 5 variables:
# \describe{
# \item{baso_perc}{coefficient for estimating basophils}
# \item{eos_perc}{coefficient for estimating eosinophils}
# \item{lymph_perc}{coefficient for estimating lymphocytes}
# \item{mono_perc}{coefficient for estimating monocytes}
# \item{neut_perc}{coefficient for estimating neutrophils}
#
# @usage data(DNAmPredictorCoef)
#
NULL
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