xDefineGenomicAnno: Function to define genomic annotations

Description Usage Arguments Value Note See Also Examples

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")

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

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

2. ENCODE DNaseI Hypersensitivity site data

3. ENCODE Histone Modification ChIP-seq data from different sources

4. FANTOM5 expressed enhancer atlas

5. ENCODE combined (ChromHMM and Segway) Genome Segmentation data

6. Conserved TFBS

7. TargetScan miRNA regulatory sites

8. TCGA exome mutation data

9. ReMap integration of transcription factor ChIP-seq data (publicly available and ENCODE)

10. Blueprint Histone Modification ChIP-seq data

11. BLUEPRINT DNaseI Hypersensitivity site data

12. BLUEPRINT DNA Methylation data

13. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (blood and T cells)

14. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (HSC and B cells)

15. CpG annotation

16. Genic annotation

17. FANTOM5 sample-ontology-enriched CAT genes

18. FANTOM5 trait-associated CAT genes

19. GWAS Catalog trait-associated SNPs

20. Roadmap Epigenomics DNase-seq peaks

See Also

xEnrichViewer

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 June 18, 2019, 3:01 p.m.

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