xDefineGenomicAnno: Function to define genomic annotations
In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description
Usage
Arguments
Value
Note
See Also
Examples
View source: R/xDefineGenomicAnno.r
Description
xDefineGenomicAnno is supposed to define genomic annotations. It
returns an object of class "GenomicRangesList" (GRL).
Usage
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xDefineGenomicAnno(
GR.annotation = c(NA, "Uniform_TFBS", "ENCODE_TFBS_ClusteredV3",
"ENCODE_TFBS_ClusteredV3_CellTypes", "Uniform_DNaseI_HS",
"ENCODE_DNaseI_ClusteredV3",
"ENCODE_DNaseI_ClusteredV3_CellTypes", "Broad_Histone", "SYDH_Histone",
"UW_Histone",
"FANTOM5_Enhancer_Cell", "FANTOM5_Enhancer_Tissue",
"FANTOM5_Enhancer_Extensive",
"FANTOM5_Enhancer", "Segment_Combined_Gm12878",
"Segment_Combined_H1hesc",
"Segment_Combined_Helas3", "Segment_Combined_Hepg2",
"Segment_Combined_Huvec",
"Segment_Combined_K562", "TFBS_Conserved", "TS_miRNA", "TCGA",
"ReMap_Public_TFBS", "ReMap_Encode_TFBS", "ReMap_PublicAndEncode_TFBS",
"ReMap_Public_mergedTFBS", "ReMap_Encode_mergedTFBS",
"ReMap_PublicAndEncode_mergedTFBS", "Blueprint_BoneMarrow_Histone",
"Blueprint_CellLine_Histone", "Blueprint_CordBlood_Histone",
"Blueprint_Thymus_Histone", "Blueprint_VenousBlood_Histone",
"Blueprint_DNaseI",
"Blueprint_Methylation_hyper", "Blueprint_Methylation_hypo",
"EpigenomeAtlas_15Segments_E029", "EpigenomeAtlas_15Segments_E030",
"EpigenomeAtlas_15Segments_E031", "EpigenomeAtlas_15Segments_E032",
"EpigenomeAtlas_15Segments_E033", "EpigenomeAtlas_15Segments_E034",
"EpigenomeAtlas_15Segments_E035", "EpigenomeAtlas_15Segments_E036",
"EpigenomeAtlas_15Segments_E037", "EpigenomeAtlas_15Segments_E038",
"EpigenomeAtlas_15Segments_E039", "EpigenomeAtlas_15Segments_E040",
"EpigenomeAtlas_15Segments_E041", "EpigenomeAtlas_15Segments_E042",
"EpigenomeAtlas_15Segments_E043", "EpigenomeAtlas_15Segments_E044",
"EpigenomeAtlas_15Segments_E045", "EpigenomeAtlas_15Segments_E046",
"EpigenomeAtlas_15Segments_E047", "EpigenomeAtlas_15Segments_E048",
"EpigenomeAtlas_15Segments_E050", "EpigenomeAtlas_15Segments_E051",
"EpigenomeAtlas_15Segments_E062", "CpG_anno", "Genic_anno",
"FANTOM5_CAT_Cell",
"FANTOM5_CAT_Tissue", "FANTOM5_CAT_DO", "FANTOM5_CAT_EFO",
"FANTOM5_CAT_HPO",
"FANTOM5_CAT_MESH", "FANTOM5_CAT_PICS", "EpigenomeAtlas_DNaseNarrow",
"EpigenomeAtlas_DNaseBroad"),
verbose = T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)
Arguments
GR.annotation
the genomic regions of annotation data. By
default, it is 'NA' to disable this option. Pre-built genomic
annotation data are detailed in the section 'Note'. Alternatively, the
user can also directly provide a customised GR object (or a list of GR
objects or a GRL object)
verbose
logical to indicate whether the messages will be
displayed in the screen. By default, it sets to false for no display
RData.location
the characters to tell the location of built-in
RData files. See xRDataLoader for details
guid
a valid (5-character) Global Unique IDentifier for an OSF
project. See xRDataLoader for details
Value
a GRL object
Note
The genomic annotation data are described below according to the data
sources and data types.
1. ENCODE Transcription Factor ChIP-seq data
Uniform_TFBS: a list (690 combinations of cell types and
transcription factors) of GenomicRanges objects; each is an GR object
containing uniformly identified peaks per cell type per transcription
factor.
ENCODE_TFBS_ClusteredV3: a list (161 transcription
factors) of GenomicRanges objects; each is an GR object containing
clustered peaks per transcription factor, along with a meta-column
'cells' telling cell types associtated with a clustered peak.
ENCODE_TFBS_ClusteredV3_CellTypes: a list (91 cell types)
of a list (transcription factors) of GenomicRanges objects. Each cell
type is a list (transcription factor) of GenomicRanges objects; each is
an GR object containing clustered peaks per transcription factor.
2. ENCODE DNaseI Hypersensitivity site data
Uniform_DNaseI_HS: a list (125 cell types) of
GenomicRanges objects; each is an GR object containing uniformly
identified peaks per cell type.
ENCODE_DNaseI_ClusteredV3: an GR object containing
clustered peaks, along with a meta-column 'num_cells' telling how many
cell types associtated with a clustered peak.
ENCODE_DNaseI_ClusteredV3_CellTypes: a list (125 cell
types) of GenomicRanges objects; each is an GR object containing
clustered peaks per cell type.
3. ENCODE Histone Modification ChIP-seq data from different sources
Broad_Histone: a list (156 combinations of cell types and
histone modifications) of GenomicRanges objects; each is an GR object
containing identified peaks per cell type and per histone modification.
This dataset was generated from ENCODE/Broad Institute.
SYDH_Histone: a list (29 combinations of cell types and
histone modifications) of GenomicRanges objects; each is an GR object
containing identified peaks per cell type and per histone modification.
This dataset was generated from ENCODE/Stanford/Yale/Davis/Harvard.
UW_Histone: a list (172 combinations of cell types and
histone modifications) of GenomicRanges objects; each is an GR object
containing identified peaks per cell type and per histone modification.
This dataset was generated from ENCODE/University of Washington.
4. FANTOM5 expressed enhancer atlas
FANTOM5_Enhancer_Cell: a list (71 cell types) of
GenomicRanges objects; each is an GR object containing enhancers
specifically expressed in a cell type.
FANTOM5_Enhancer_Tissue: a list (41 tissues) of
GenomicRanges objects; each is an GR object containing enhancers
specifically expressed in a tissue.
FANTOM5_Enhancer_Extensive: a list (5 categories of
extensitive enhancers) of GenomicRanges objects; each is an GR object
containing extensitive enhancers. They are:
"Extensive_ubiquitous_enhancers_cells" for ubiquitous enhancers
expressed over the entire set of cell types;
"Extensive_ubiquitous_enhancers_organs" for ubiquitous enhancers
expressed over the entire set of tissues;
"Extensive_enhancers_tss_associations" for TSS-enhancer
associations(RefSeq promoters only); "Extensive_permissive_enhancers"
and "Extensive_robust_enhancers" for permissive and robust enhancer
sets.
FANTOM5_Enhancer: a list (117 cell
types/tissues/categories) of GenomicRanges objects; each is an GR
object.
5. ENCODE combined (ChromHMM and Segway) Genome Segmentation data
Segment_Combined_Gm12878: a list (7 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the cell line GM12878 (a lymphoblastoid cell
line).
Segment_Combined_H1hesc: a list (7 categories of segments)
of GenomicRanges objects; each is an GR object containing segments per
category in the cell line H1-hESC (H1 human embryonic stem cells).
Segment_Combined_Helas3: a list (7 categories of segments)
of GenomicRanges objects; each is an GR object containing segments per
category in the cell line HeLa S3.
Segment_Combined_Hepg2: a list (7 categories of segments)
of GenomicRanges objects; each is an GR object containing segments per
category in the cell line HepG2 (liver hepatocellular carcinoma).
Segment_Combined_Huvec: a list (7 categories of segments)
of GenomicRanges objects; each is an GR object containing segments per
category in the cell line HUVEC (Human Umbilical Vein Endothelial
Cells).
Segment_Combined_K562: a list (7 categories of segments)
of GenomicRanges objects; each is an GR object containing segments per
category in the cell line K562 (human erythromyeloblastoid leukemia
cell line).
6. Conserved TFBS
TFBS_Conserved: a list (245 PWM) of GenomicRanges objects;
each is an GR object containing human/mouse/rat conserved TFBS for each
PWM.
7. TargetScan miRNA regulatory sites
TS_miRNA: a list (153 miRNA) of GenomicRanges objects;
each is an GR object containing miRNA regulatory sites for each miRNA.
8. TCGA exome mutation data
TCGA: a list (11 tumor types) of GenomicRanges objects;
each is an GR object containing exome mutation across tumor patients of
the same tumor type.
9. ReMap integration of transcription factor ChIP-seq data (publicly
available and ENCODE)
ReMap_Public_TFBS: a list (1759 combinations of GSE
studies and transcription factors and cell types) of GenomicRanges
objects; each is an GR object containing identified peaks per GSE study
per transcripton factor per cell type.
ReMap_Encode_TFBS: a list (1066 combinations of ENCODE
transcription factors and cell types) of GenomicRanges objects; each is
an GR object containing identified peaks per ENCODE study per
transcripton factor per cell type.
ReMap_PublicAndEncode_TFBS: a list (2825 combinations of
GSE/ENCODE studies and transcription factors and cell types) of
GenomicRanges objects; each is an GR object containing identified peaks
per GSE/ENCODE study per transcripton factor per cell type.
ReMap_Public_mergedTFBS: a list (331 transcription factors
under GSE studies) of GenomicRanges objects; each is an GR object
containing merged peaks per transcripton factor.
ReMap_Encode_mergedTFBS: a list (279 transcription factors
under ENCODE) of GenomicRanges objects; each is an GR object containing
merged peaks per transcripton factor.
ReMap_PublicAndEncode_mergedTFBS: a list (485
transcription factors under GSE studies and ENCODE) of GenomicRanges
objects; each is an GR object containing identified peaks per
transcripton factor.
10. Blueprint Histone Modification ChIP-seq data
Blueprint_BoneMarrow_Histone: a list (132 combinations of
histone modifications and samples) of GenomicRanges objects; each is an
GR object containing identified peaks per histone per sample (from bone
marrow).
Blueprint_CellLine_Histone: a list (38 combinations of
histone modifications and cell lines) of GenomicRanges objects; each is
an GR object containing identified peaks per histone per cell line.
Blueprint_CordBlood_Histone: a list (126 combinations of
histone modifications and samples) of GenomicRanges objects; each is an
GR object containing identified peaks per histone per sample (from cord
blood).
Blueprint_Thymus_Histone: a list (5 combinations of
histone modifications and samples) of GenomicRanges objects; each is an
GR object containing identified peaks per histone per sample (from
thymus).
Blueprint_VenousBlood_Histone: a list (296 combinations of
histone modifications and samples) of GenomicRanges objects; each is an
GR object containing identified peaks per histone per sample (from
venous blood).
11. BLUEPRINT DNaseI Hypersensitivity site data
Blueprint_DNaseI: a list (36 samples) of GenomicRanges
objects; each is an GR object containing identified peaks per sample.
12. BLUEPRINT DNA Methylation data
Blueprint_Methylation_hyper: a list (206 samples) of
GenomicRanges objects; each is an GR object containing hyper-methylated
CpG regions per sample.
Blueprint_Methylation_hypo: a list (206 samples) of
GenomicRanges objects; each is an GR object containing hypo-methylated
CpG regions per sample.
13. Roadmap Epigenomics Core 15-state Genome Segmentation data for
primary cells (blood and T cells)
EpigenomeAtlas_15Segments_E033: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E033 (Primary T cells
from cord blood).
EpigenomeAtlas_15Segments_E034: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E034 (Primary T cells
from peripheral blood).
EpigenomeAtlas_15Segments_E037: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E037 (Primary T helper
memory cells from peripheral blood 2).
EpigenomeAtlas_15Segments_E038: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E038 (Primary T helper
naive cells from peripheral blood).
EpigenomeAtlas_15Segments_E039: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E039 (Primary T helper
naive cells from peripheral blood).
EpigenomeAtlas_15Segments_E040: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E040 (Primary T helper
memory cells from peripheral blood 1).
EpigenomeAtlas_15Segments_E041: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E041 (Primary T helper
cells PMA-I stimulated).
EpigenomeAtlas_15Segments_E042: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E042 (Primary T helper
17 cells PMA-I stimulated).
EpigenomeAtlas_15Segments_E043: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E043 (Primary T helper
cells from peripheral blood).
EpigenomeAtlas_15Segments_E044: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E044 (Primary T
regulatory cells from peripheral blood).
EpigenomeAtlas_15Segments_E045: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E045 (Primary T cells
effector/memory enriched from peripheral blood).
EpigenomeAtlas_15Segments_E047: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E047 (Primary T killer
naive cells from peripheral blood).
EpigenomeAtlas_15Segments_E048: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E048 (Primary T killer
memory cells from peripheral blood).
EpigenomeAtlas_15Segments_E062: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E062 (Primary
mononuclear cells from peripheral blood).
14. Roadmap Epigenomics Core 15-state Genome Segmentation data for
primary cells (HSC and B cells)
EpigenomeAtlas_15Segments_E029: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E029 (Primary
monocytes from peripheral blood).
EpigenomeAtlas_15Segments_E030: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E030 (Primary
neutrophils from peripheral blood).
EpigenomeAtlas_15Segments_E031: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E031 (Primary B cells
from cord blood).
EpigenomeAtlas_15Segments_E032: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E032 (Primary B cells
from peripheral blood).
EpigenomeAtlas_15Segments_E035: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E035 (Primary
hematopoietic stem cells).
EpigenomeAtlas_15Segments_E036: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E036 (Primary
hematopoietic stem cells short term culture).
EpigenomeAtlas_15Segments_E046: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E046 (Primary Natural
Killer cells from peripheral blood).
EpigenomeAtlas_15Segments_E050: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E050 (Primary
hematopoietic stem cells G-CSF-mobilized Female).
EpigenomeAtlas_15Segments_E051: a list (15 categories of
segments) of GenomicRanges objects; each is an GR object containing
segments per category in the reference epigenome E051 (Primary
hematopoietic stem cells G-CSF-mobilized Male).
15. CpG annotation
CpG_anno: a list (4 categories) of GenomicRanges objects;
each is an GR object. They are exclusive, including (in order)
"CpG_islands", "CpG_shores" (2Kb upstream/downstream from the ends of
the CpG islands), "CpG_shelves" (2Kb upstream/downstream of the
farthest upstream/downstream limits of the CpG shores), and "CpG_inter"
(the remaining inter-CGI genomic regions 'open sea').
16. Genic annotation
Genic_anno: a list (12 categories) of GenomicRanges
objects; each is an GR object. They are not exclusively, including
"Genic_1to5kb" (1-5Kb upstream of TSS), "Genic_promoters" (1Kb upstream
of TSS), "Genic_5UTRs", "Genic_firstexons" (first exons),
"Genic_exons", "Genic_exonintronboundaries", "Genic_introns",
"Genic_intronexonboundaries", "Genic_cds", "Genic_3UTRs",
"Genic_intergenic" (the intergenic regions exclude the previous list of
annotations), and "Genic_lncRNA" (GENCODE long non-coding RNA (lncRNA)
transcripts).
17. FANTOM5 sample-ontology-enriched CAT genes
FANTOM5_CAT_Cell: a list (173 cell types) of GenomicRanges
objects; each is an GR object containing CAT genes specifically
expressed in a cell type.
FANTOM5_CAT_Tissue: a list (174 tissues) of GenomicRanges
objects; each is an GR object containing CAT genes specifically
expressed in a tissue.
18. FANTOM5 trait-associated CAT genes
FANTOM5_CAT_DO: a list (299 traits grouped by disease
ontology) of GenomicRanges objects; each is an GR object containing CAT
genes harboring at least one trait-associated SNP.
FANTOM5_CAT_EFO: a list (93 traits grouped by experiment
factor ontology) of GenomicRanges objects; each is an GR object
containing CAT genes harboring at least one trait-associated SNP.
FANTOM5_CAT_HPO: a list (176 traits grouped by human
phenotype ontology) of GenomicRanges objects; each is an GR object
containing CAT genes harboring at least one trait-associated SNP.
FANTOM5_CAT_MESH: a list (210 traits grouped by Medical
Subject Headings) of GenomicRanges objects; each is an GR object
containing CAT genes harboring at least one trait-associated SNP.
FANTOM5_CAT_PICS: a list (39 traits grouped by PICS
dieases) of GenomicRanges objects; each is an GR object containing CAT
genes harboring at least one trait-associated SNP.
19. GWAS Catalog trait-associated SNPs
GWAScatalog_alltraits: a list (390 traits grouped by EFO)
of GenomicRanges objects; each is an GR object containing
trait-associated SNPs.
GWAScatalog_bloodindex: a list (29 traits grouped by EFO)
of GenomicRanges objects; each is an GR object containing
trait-associated SNPs.
20. Roadmap Epigenomics DNase-seq peaks
EpigenomeAtlas_DNaseNarrow: a list (39 cell types) of
GenomicRanges objects; each is an GR object containing narrow Peaks in
FDR 0.01 hotspots.
EpigenomeAtlas_DNaseBroad: a list (39 cell types) of
GenomicRanges objects; each is an GR object containing broad Peaks in
FDR 0.01 hotspots.
See Also
Examples
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# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
grl <- xDefineGenomicAnno("Uniform_TFBS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("Uniform_DNaseI_HS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("FANTOM5_Enhancer_Cell",
RData.location=RData.location)
grl <- xDefineGenomicAnno("ReMap_Public_TFBS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("EpigenomeAtlas_15Segments_E029",
RData.location=RData.location)
grl <- xDefineGenomicAnno("FANTOM5_CAT_Cell",
RData.location=RData.location)
grl <- xDefineGenomicAnno("GWAScatalog_alltraits",
RData.location=RData.location)
# the customised
## a GR object
GR.annotation <- grl[[1]]
grl_customised <- xDefineGenomicAnno(GR.annotation,
RData.location=RData.location)
## a list of GR objects
GR.annotation <- lapply(grl[1:2], function(x) x)
grl_customised <- xDefineGenomicAnno(GR.annotation,
RData.location=RData.location)
## End(Not run)
XGR documentation built on Jan. 8, 2020, 5:06 p.m.
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Description Usage Arguments Value Note See Also Examples
View source: R/xDefineGenomicAnno.r
Description
xDefineGenomicAnno is supposed to define genomic annotations. It
returns an object of class "GenomicRangesList" (GRL).
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | xDefineGenomicAnno(
GR.annotation = c(NA, "Uniform_TFBS", "ENCODE_TFBS_ClusteredV3",
"ENCODE_TFBS_ClusteredV3_CellTypes", "Uniform_DNaseI_HS",
"ENCODE_DNaseI_ClusteredV3",
"ENCODE_DNaseI_ClusteredV3_CellTypes", "Broad_Histone", "SYDH_Histone",
"UW_Histone",
"FANTOM5_Enhancer_Cell", "FANTOM5_Enhancer_Tissue",
"FANTOM5_Enhancer_Extensive",
"FANTOM5_Enhancer", "Segment_Combined_Gm12878",
"Segment_Combined_H1hesc",
"Segment_Combined_Helas3", "Segment_Combined_Hepg2",
"Segment_Combined_Huvec",
"Segment_Combined_K562", "TFBS_Conserved", "TS_miRNA", "TCGA",
"ReMap_Public_TFBS", "ReMap_Encode_TFBS", "ReMap_PublicAndEncode_TFBS",
"ReMap_Public_mergedTFBS", "ReMap_Encode_mergedTFBS",
"ReMap_PublicAndEncode_mergedTFBS", "Blueprint_BoneMarrow_Histone",
"Blueprint_CellLine_Histone", "Blueprint_CordBlood_Histone",
"Blueprint_Thymus_Histone", "Blueprint_VenousBlood_Histone",
"Blueprint_DNaseI",
"Blueprint_Methylation_hyper", "Blueprint_Methylation_hypo",
"EpigenomeAtlas_15Segments_E029", "EpigenomeAtlas_15Segments_E030",
"EpigenomeAtlas_15Segments_E031", "EpigenomeAtlas_15Segments_E032",
"EpigenomeAtlas_15Segments_E033", "EpigenomeAtlas_15Segments_E034",
"EpigenomeAtlas_15Segments_E035", "EpigenomeAtlas_15Segments_E036",
"EpigenomeAtlas_15Segments_E037", "EpigenomeAtlas_15Segments_E038",
"EpigenomeAtlas_15Segments_E039", "EpigenomeAtlas_15Segments_E040",
"EpigenomeAtlas_15Segments_E041", "EpigenomeAtlas_15Segments_E042",
"EpigenomeAtlas_15Segments_E043", "EpigenomeAtlas_15Segments_E044",
"EpigenomeAtlas_15Segments_E045", "EpigenomeAtlas_15Segments_E046",
"EpigenomeAtlas_15Segments_E047", "EpigenomeAtlas_15Segments_E048",
"EpigenomeAtlas_15Segments_E050", "EpigenomeAtlas_15Segments_E051",
"EpigenomeAtlas_15Segments_E062", "CpG_anno", "Genic_anno",
"FANTOM5_CAT_Cell",
"FANTOM5_CAT_Tissue", "FANTOM5_CAT_DO", "FANTOM5_CAT_EFO",
"FANTOM5_CAT_HPO",
"FANTOM5_CAT_MESH", "FANTOM5_CAT_PICS", "EpigenomeAtlas_DNaseNarrow",
"EpigenomeAtlas_DNaseBroad"),
verbose = T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)
|
Arguments
GR.annotation |
the genomic regions of annotation data. By default, it is 'NA' to disable this option. Pre-built genomic annotation data are detailed in the section 'Note'. Alternatively, the user can also directly provide a customised GR object (or a list of GR objects or a GRL object) |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display |
RData.location |
the characters to tell the location of built-in
RData files. See |
guid |
a valid (5-character) Global Unique IDentifier for an OSF
project. See |
Value
a GRL object
Note
The genomic annotation data are described below according to the data
sources and data types.
1. ENCODE Transcription Factor ChIP-seq data
Uniform_TFBS: a list (690 combinations of cell types and transcription factors) of GenomicRanges objects; each is an GR object containing uniformly identified peaks per cell type per transcription factor.ENCODE_TFBS_ClusteredV3: a list (161 transcription factors) of GenomicRanges objects; each is an GR object containing clustered peaks per transcription factor, along with a meta-column 'cells' telling cell types associtated with a clustered peak.ENCODE_TFBS_ClusteredV3_CellTypes: a list (91 cell types) of a list (transcription factors) of GenomicRanges objects. Each cell type is a list (transcription factor) of GenomicRanges objects; each is an GR object containing clustered peaks per transcription factor.
2. ENCODE DNaseI Hypersensitivity site data
Uniform_DNaseI_HS: a list (125 cell types) of GenomicRanges objects; each is an GR object containing uniformly identified peaks per cell type.ENCODE_DNaseI_ClusteredV3: an GR object containing clustered peaks, along with a meta-column 'num_cells' telling how many cell types associtated with a clustered peak.ENCODE_DNaseI_ClusteredV3_CellTypes: a list (125 cell types) of GenomicRanges objects; each is an GR object containing clustered peaks per cell type.
3. ENCODE Histone Modification ChIP-seq data from different sources
Broad_Histone: a list (156 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/Broad Institute.SYDH_Histone: a list (29 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/Stanford/Yale/Davis/Harvard.UW_Histone: a list (172 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/University of Washington.
4. FANTOM5 expressed enhancer atlas
FANTOM5_Enhancer_Cell: a list (71 cell types) of GenomicRanges objects; each is an GR object containing enhancers specifically expressed in a cell type.FANTOM5_Enhancer_Tissue: a list (41 tissues) of GenomicRanges objects; each is an GR object containing enhancers specifically expressed in a tissue.FANTOM5_Enhancer_Extensive: a list (5 categories of extensitive enhancers) of GenomicRanges objects; each is an GR object containing extensitive enhancers. They are: "Extensive_ubiquitous_enhancers_cells" for ubiquitous enhancers expressed over the entire set of cell types; "Extensive_ubiquitous_enhancers_organs" for ubiquitous enhancers expressed over the entire set of tissues; "Extensive_enhancers_tss_associations" for TSS-enhancer associations(RefSeq promoters only); "Extensive_permissive_enhancers" and "Extensive_robust_enhancers" for permissive and robust enhancer sets.FANTOM5_Enhancer: a list (117 cell types/tissues/categories) of GenomicRanges objects; each is an GR object.
5. ENCODE combined (ChromHMM and Segway) Genome Segmentation data
Segment_Combined_Gm12878: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line GM12878 (a lymphoblastoid cell line).Segment_Combined_H1hesc: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line H1-hESC (H1 human embryonic stem cells).Segment_Combined_Helas3: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HeLa S3.Segment_Combined_Hepg2: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HepG2 (liver hepatocellular carcinoma).Segment_Combined_Huvec: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HUVEC (Human Umbilical Vein Endothelial Cells).Segment_Combined_K562: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line K562 (human erythromyeloblastoid leukemia cell line).
6. Conserved TFBS
TFBS_Conserved: a list (245 PWM) of GenomicRanges objects; each is an GR object containing human/mouse/rat conserved TFBS for each PWM.
7. TargetScan miRNA regulatory sites
TS_miRNA: a list (153 miRNA) of GenomicRanges objects; each is an GR object containing miRNA regulatory sites for each miRNA.
8. TCGA exome mutation data
TCGA: a list (11 tumor types) of GenomicRanges objects; each is an GR object containing exome mutation across tumor patients of the same tumor type.
9. ReMap integration of transcription factor ChIP-seq data (publicly available and ENCODE)
ReMap_Public_TFBS: a list (1759 combinations of GSE studies and transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per GSE study per transcripton factor per cell type.ReMap_Encode_TFBS: a list (1066 combinations of ENCODE transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per ENCODE study per transcripton factor per cell type.ReMap_PublicAndEncode_TFBS: a list (2825 combinations of GSE/ENCODE studies and transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per GSE/ENCODE study per transcripton factor per cell type.ReMap_Public_mergedTFBS: a list (331 transcription factors under GSE studies) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.ReMap_Encode_mergedTFBS: a list (279 transcription factors under ENCODE) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.ReMap_PublicAndEncode_mergedTFBS: a list (485 transcription factors under GSE studies and ENCODE) of GenomicRanges objects; each is an GR object containing identified peaks per transcripton factor.
10. Blueprint Histone Modification ChIP-seq data
Blueprint_BoneMarrow_Histone: a list (132 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from bone marrow).Blueprint_CellLine_Histone: a list (38 combinations of histone modifications and cell lines) of GenomicRanges objects; each is an GR object containing identified peaks per histone per cell line.Blueprint_CordBlood_Histone: a list (126 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from cord blood).Blueprint_Thymus_Histone: a list (5 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from thymus).Blueprint_VenousBlood_Histone: a list (296 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from venous blood).
11. BLUEPRINT DNaseI Hypersensitivity site data
Blueprint_DNaseI: a list (36 samples) of GenomicRanges objects; each is an GR object containing identified peaks per sample.
12. BLUEPRINT DNA Methylation data
Blueprint_Methylation_hyper: a list (206 samples) of GenomicRanges objects; each is an GR object containing hyper-methylated CpG regions per sample.Blueprint_Methylation_hypo: a list (206 samples) of GenomicRanges objects; each is an GR object containing hypo-methylated CpG regions per sample.
13. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (blood and T cells)
EpigenomeAtlas_15Segments_E033: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E033 (Primary T cells from cord blood).EpigenomeAtlas_15Segments_E034: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E034 (Primary T cells from peripheral blood).EpigenomeAtlas_15Segments_E037: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E037 (Primary T helper memory cells from peripheral blood 2).EpigenomeAtlas_15Segments_E038: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E038 (Primary T helper naive cells from peripheral blood).EpigenomeAtlas_15Segments_E039: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E039 (Primary T helper naive cells from peripheral blood).EpigenomeAtlas_15Segments_E040: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E040 (Primary T helper memory cells from peripheral blood 1).EpigenomeAtlas_15Segments_E041: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E041 (Primary T helper cells PMA-I stimulated).EpigenomeAtlas_15Segments_E042: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E042 (Primary T helper 17 cells PMA-I stimulated).EpigenomeAtlas_15Segments_E043: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E043 (Primary T helper cells from peripheral blood).EpigenomeAtlas_15Segments_E044: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E044 (Primary T regulatory cells from peripheral blood).EpigenomeAtlas_15Segments_E045: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E045 (Primary T cells effector/memory enriched from peripheral blood).EpigenomeAtlas_15Segments_E047: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E047 (Primary T killer naive cells from peripheral blood).EpigenomeAtlas_15Segments_E048: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E048 (Primary T killer memory cells from peripheral blood).EpigenomeAtlas_15Segments_E062: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E062 (Primary mononuclear cells from peripheral blood).
14. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (HSC and B cells)
EpigenomeAtlas_15Segments_E029: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E029 (Primary monocytes from peripheral blood).EpigenomeAtlas_15Segments_E030: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E030 (Primary neutrophils from peripheral blood).EpigenomeAtlas_15Segments_E031: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E031 (Primary B cells from cord blood).EpigenomeAtlas_15Segments_E032: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E032 (Primary B cells from peripheral blood).EpigenomeAtlas_15Segments_E035: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E035 (Primary hematopoietic stem cells).EpigenomeAtlas_15Segments_E036: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E036 (Primary hematopoietic stem cells short term culture).EpigenomeAtlas_15Segments_E046: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E046 (Primary Natural Killer cells from peripheral blood).EpigenomeAtlas_15Segments_E050: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E050 (Primary hematopoietic stem cells G-CSF-mobilized Female).EpigenomeAtlas_15Segments_E051: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E051 (Primary hematopoietic stem cells G-CSF-mobilized Male).
15. CpG annotation
CpG_anno: a list (4 categories) of GenomicRanges objects; each is an GR object. They are exclusive, including (in order) "CpG_islands", "CpG_shores" (2Kb upstream/downstream from the ends of the CpG islands), "CpG_shelves" (2Kb upstream/downstream of the farthest upstream/downstream limits of the CpG shores), and "CpG_inter" (the remaining inter-CGI genomic regions 'open sea').
16. Genic annotation
Genic_anno: a list (12 categories) of GenomicRanges objects; each is an GR object. They are not exclusively, including "Genic_1to5kb" (1-5Kb upstream of TSS), "Genic_promoters" (1Kb upstream of TSS), "Genic_5UTRs", "Genic_firstexons" (first exons), "Genic_exons", "Genic_exonintronboundaries", "Genic_introns", "Genic_intronexonboundaries", "Genic_cds", "Genic_3UTRs", "Genic_intergenic" (the intergenic regions exclude the previous list of annotations), and "Genic_lncRNA" (GENCODE long non-coding RNA (lncRNA) transcripts).
17. FANTOM5 sample-ontology-enriched CAT genes
FANTOM5_CAT_Cell: a list (173 cell types) of GenomicRanges objects; each is an GR object containing CAT genes specifically expressed in a cell type.FANTOM5_CAT_Tissue: a list (174 tissues) of GenomicRanges objects; each is an GR object containing CAT genes specifically expressed in a tissue.
18. FANTOM5 trait-associated CAT genes
FANTOM5_CAT_DO: a list (299 traits grouped by disease ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.FANTOM5_CAT_EFO: a list (93 traits grouped by experiment factor ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.FANTOM5_CAT_HPO: a list (176 traits grouped by human phenotype ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.FANTOM5_CAT_MESH: a list (210 traits grouped by Medical Subject Headings) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.FANTOM5_CAT_PICS: a list (39 traits grouped by PICS dieases) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.
19. GWAS Catalog trait-associated SNPs
GWAScatalog_alltraits: a list (390 traits grouped by EFO) of GenomicRanges objects; each is an GR object containing trait-associated SNPs.GWAScatalog_bloodindex: a list (29 traits grouped by EFO) of GenomicRanges objects; each is an GR object containing trait-associated SNPs.
20. Roadmap Epigenomics DNase-seq peaks
EpigenomeAtlas_DNaseNarrow: a list (39 cell types) of GenomicRanges objects; each is an GR object containing narrow Peaks in FDR 0.01 hotspots.EpigenomeAtlas_DNaseBroad: a list (39 cell types) of GenomicRanges objects; each is an GR object containing broad Peaks in FDR 0.01 hotspots.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | # Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
grl <- xDefineGenomicAnno("Uniform_TFBS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("Uniform_DNaseI_HS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("FANTOM5_Enhancer_Cell",
RData.location=RData.location)
grl <- xDefineGenomicAnno("ReMap_Public_TFBS",
RData.location=RData.location)
grl <- xDefineGenomicAnno("EpigenomeAtlas_15Segments_E029",
RData.location=RData.location)
grl <- xDefineGenomicAnno("FANTOM5_CAT_Cell",
RData.location=RData.location)
grl <- xDefineGenomicAnno("GWAScatalog_alltraits",
RData.location=RData.location)
# the customised
## a GR object
GR.annotation <- grl[[1]]
grl_customised <- xDefineGenomicAnno(GR.annotation,
RData.location=RData.location)
## a list of GR objects
GR.annotation <- lapply(grl[1:2], function(x) x)
grl_customised <- xDefineGenomicAnno(GR.annotation,
RData.location=RData.location)
## End(Not run)
|
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