XGR (version 1.1.5)

xDefineGenomicAnno: Function to define genomic annotations

Description

xDefineGenomicAnno is supposed to define genomic annotations. It returns an object of class "GenomicRangesList" (GRL).

Usage

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

See Also

xEnrichViewer

Examples

# NOT RUN {
# 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)
# }