R/data.R

In Yi-Jiang/MethyGenotyper: MethylGenotyper: Accurate estimation of SNP genotypes from DNA methylation data

#' EPIC manifest file
#' 
#' A dataset containing all EPIC probes information.
#' 
#' @usage data(mnfst)
#' @format A data frame with 866554 rows and 5 columns:
#' \describe{
#'  \item{Name}{CpG name}
#'  \item{AddressA_ID}{AdressA ID}
#'  \item{AddressB_ID}{AdressB ID}
#'  \item{Infinium_Design_Type}{Infinium design type}
#'  \item{Color_Channel}{Color channel}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"mnfst"

#' 450K manifest file
#' 
#' A dataset containing all 450K probes information.
#' 
#' @usage data(mnfst_450K)
#' @format A data frame with 486428 rows and 5 columns:
#' \describe{
#'  \item{Name}{CpG name}
#'  \item{AddressA_ID}{AdressA ID}
#'  \item{AddressB_ID}{AdressB ID}
#'  \item{Infinium_Design_Type}{Infinium design type}
#'  \item{Color_Channel}{Color channel}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/humanmethylation450/humanmethylation450_15017482_v1-2.csv}
"mnfst_450K"

#' SNP probe information for EPIC
#' 
#' A dataset containing SNP probe information. Only autosome probes are included.
#' 
#' @usage data(probeInfo_snp)
#' @format A data frame with 53 rows and 14 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{Probe types, color channel, and signal corresponds to alternative allele}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_snp"

#' SNP probe information for 450K
#' 
#' A dataset containing SNP probe information. Only autosome probes are included.
#' 
#' @usage data(probeInfo_snp_450K)
#' @format A data frame with 57 rows and 14 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{Probe types, color channel, and signal corresponds to alternative allele}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_snp_450K"

#' Type I probe information for EPIC
#' 
#' A dataset containing Type I probe information.
#' 
#' @usage data(probeInfo_typeI)
#' @format A data frame with 715 rows and 16 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{NA}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#'  \item{loc_pass}{Passed peak position test or not}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_typeI"

#' Type I probe information for 450K
#' 
#' A dataset containing Type I probe information.
#' 
#' @usage data(probeInfo_typeI_450K)
#' @format A data frame with 712 rows and 14 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{NA}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_typeI_450K"

#' Type II probe information for EPIC
#' 
#' A dataset containing information of Type II probes with SNPs at the extension bases. We only consider the situation that the alternative allele is A/T and the reference allele is C/G.
#' 
#' @usage data(probeInfo_typeII)
#' @format A data frame with 26420 rows and 16 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{Probe types, color channel, and signal corresponds to alternative allele}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#'  \item{loc_pass}{Passed peak position test or not}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_typeII"

#' Type II probe information for 450K
#' 
#' A dataset containing information of Type II probes with SNPs at the extension bases. We only consider the situation that the alternative allele is A/T and the reference allele is C/G.
#' 
#' @usage data(probeInfo_typeII_450K)
#' @format A data frame with 11875 rows and 14 columns:
#' \describe{
#'  \item{Chr}{Chromosome ID}
#'  \item{Pos}{Position}
#'  \item{SNP}{SNP ID targeted by the CpG}
#'  \item{RefAllele}{Reference allele}
#'  \item{AltAllele}{Alternative allele}
#'  \item{CpG}{CpG}
#'  \item{Color}{Color channel}
#'  \item{Group}{Probe types, color channel, and signal corresponds to alternative allele}
#'  \item{ALL_AF}{Allele frequency of all population}
#'  \item{EAS_AF}{Allele frequency of East Asian}
#'  \item{AMR_AF}{Allele frequency of American}
#'  \item{AFR_AF}{Allele frequency of African}
#'  \item{EUR_AF}{Allele frequency of European}
#'  \item{SAS_AF}{Allele frequency of South Asian}
#' }
#' @source \url{https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip}
"probeInfo_typeII_450K"

#' Probe list for EPIC
#' 
#' A dataset containing the list of 53 SNP probes on autosomes, 715 Type I probes, and 26420 type II probes.
#' 
#' @usage data(probelist)
#' @format A data frame with 27188 rows and 2 columns:
#' \describe{
#'  \item{CpG}{CpG list}
#'  \item{Type}{Probe types}
#'  \item{A2}{Alternative alleles}
#' }
"probelist"

#' Probe list for 450K
#' 
#' A dataset containing the list of 53 SNP probes on autosomes, 712 Type I probes, and 11875 type II probes.
#' 
#' @usage data(probelist_450K)
#' @format A data frame with 12644 rows and 2 columns:
#' \describe{
#'  \item{CpG}{CpG list}
#'  \item{Type}{Probe types}
#' }
"probelist_450K"

#' Reference genotypes in the 1000 Genomes Project
#' 
#' A matrix of reference genotypes in the 1000 Genomes Project (1KGP). It contains 2504 samples and 28,619 SNPs overlapping the methylation probes.
#' 
#' @usage data(refGeno_1KGP3)
#' @format A matrix with 28,619 rows and 2504 columns:
#' \describe{
#'  \item{Row}{SNPs overlapping the methylation probes}
#'  \item{Column}{Samples}
#' }
"refGeno_1KGP3"

#' SNPs in 1KGP with HWE<1e-20 or F_MISSING>=0.05
#' 
#' SNPs to be removed in TRACE PCA
#' 
#' @usage data(refGeno_1KGP3_SNP_failQC)
#' @format A vector with 491 items:
#' \describe{
#'  \item{Value}{SNP rs ID}
#' }
"refGeno_1KGP3_SNP_failQC"

#' Population information for the 1KGP samples
#' 
#' A vector of population information for the 2504 samples in 1KGP.
#' 
#' @usage data(sam2pop)
#' @format A vector with 2504 items:
#' \describe{
#'  \item{Name}{Sample ID}
#'  \item{Value}{Population}
#' }
"sam2pop"