xGRviaGenomicAnnoAdv: Function to conduct region-based enrichment analysis using genomic annotations via sampling

Description

xGRviaGenomicAnnoAdv is supposed to conduct region-based enrichment analysis for the input genomic region data (genome build h19), using genomic annotations (eg active chromatin, transcription factor binding sites/motifs, conserved sites). Enrichment analysis is achieved by comparing the observed overlaps against the expected overlaps which are estimated from the null distribution. The null distribution is generated via sampling, that is, randomly generating samples for data genomic regions from background genomic regions. Background genomic regions can be provided by the user; by default, the annotatable genomic regions will be used.

Usage

xGRviaGenomicAnnoAdv(data.file, annotation.file = NULL,
background.file = NULL, format.file = c("data.frame", "bed",
"chr:start-end", "GRanges"), build.conversion = c(NA, "hg38.to.hg19",
"hg18.to.hg19"), background.annotatable.only = F, num.samples = 1000,
gap.max = 50000, max.distance = NULL, p.adjust.method = c("BH", "BY",
"bonferroni", "holm", "hochberg", "hommel"), 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_Public_mergedTFBS",
"ReMap_PublicAndEncode_mergedTFBS", "ReMap_Encode_TFBS",
"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"), parallel = TRUE, multicores = NULL,
verbose = T, RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

data.file

an input data file, containing a list of genomic regions to test. If the input file is formatted as a 'data.frame' (specified by the parameter 'format.file' below), the first three columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), and the ending chromosome position (3rd column). If the format is indicated as 'bed' (browser extensible data), the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the genomic regions provided are not ranged but only the single position, the ending chromosome position (3rd column) is allowed not to be provided. If the format is indicated as "chr:start-end", instead of using the first 3 columns, only the first column will be used and processed. If the file also contains other columns, these additional columns will be ignored. Alternatively, the input file can be the content itself assuming that input file has been read. Note: the file should use the tab delimiter as the field separator between columns.

annotation.file

an input annotation file containing genomic annotations for genomic regions. If the input file is formatted as a 'data.frame', the first four columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), the ending chromosome position (3rd column), and the genomic annotations (eg transcription factors and histones; 4th column). If the format is indicated as 'bed', the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the format is indicated as "chr:start-end", the first two columns correspond to the chromosome:start-end (1st column) and the genomic annotations (eg transcription factors and histones; 2nd column). If the file also contains other columns, these additional columns will be ignored. Alternatively, the input file can be the content itself assuming that input file has been read. Note: the file should use the tab delimiter as the field separator between columns.

background.file

an input background file containing a list of genomic regions as the test background. The file format is the same as 'data.file'. By default, it is NULL meaning all annotatable bases (ig non-redundant bases covered by 'annotation.file') are used as background. However, if only one annotation (eg only a transcription factor) is provided in 'annotation.file', the background must be provided.

format.file

the format for input files. It can be one of "data.frame", "chr:start-end", "bed" and "GRanges"

build.conversion

the conversion from one genome build to another. The conversions supported are "hg38.to.hg19" and "hg18.to.hg19". By default it is NA (no need to do so).

background.annotatable.only

logical to indicate whether the background is further restricted to annotatable bases (covered by 'annotation.file'). In other words, if the background is provided, the background bases are those after being overlapped with annotatable bases. Notably, if only one annotation (eg only a transcription factor) is provided in 'annotation.file', it should be false.

num.samples

the number of samples randomly generated

gap.max

the maximum distance of background islands to be considered away from data regions. Only background islands no far way from this distance will be considered. For example, if it is 0, meaning that only background islands that overlapp with genomic regions will be considered. By default, it is 50000

max.distance

the maximum distance away from data regions that is allowed when generating random samples. By default, it is NULl meaning no such restriction

p.adjust.method

the method used to adjust p-values. It can be one of "BH", "BY", "bonferroni", "holm", "hochberg" and "hommel". The first two methods "BH" (widely used) and "BY" control the false discovery rate (FDR: the expected proportion of false discoveries amongst the rejected hypotheses); the last four methods "bonferroni", "holm", "hochberg" and "hommel" are designed to give strong control of the family-wise error rate (FWER). Notes: FDR is a less stringent condition than FWER

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'. Beyond pre-built annotation data, the user can specify the customised input. To do so, first save your RData file (a list of GR objects, each is an GR object correponding to an annotation) into your local computer. Then, tell "GR.annotation" with your RData file name (with or without extension), plus specify your file RData path in "RData.location". Note: you can also load your customised GR object directly

parallel

logical to indicate whether parallel computation with multicores is used. By default, it sets to true, but not necessarily does so. Partly because parallel backends available will be system-specific (now only Linux or Mac OS). Also, it will depend on whether these two packages "foreach" and "doMC" have been installed. It can be installed via:

source("http://bioconductor.org/biocLite.R");
biocLite(c("foreach","doMC"))

. If not yet installed, this option will be disabled

multicores

an integer to specify how many cores will be registered as the multicore parallel backend to the 'foreach' package. If NULL, it will use a half of cores available in a user's computer. This option only works when parallel computation is enabled

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 data frame with 8 columns:

name: the annotation name
nAnno: the number of bases covered by that annotation. If the background is provided, they are also restricted by this
nOverlap: the number of bases overlapped between input regions and annotation regions. If the background is provided, they are also restricted by this
fc: fold change
zscore: z-score
pvalue: p-value
adjp: adjusted p-value. It is the p value but after being adjusted for multiple comparisons
nData: the number of bases covered by input regions
nBG: the number of bases covered by background regions

Examples

Run this code

## 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_dev"
# 
# # Enrichment analysis for GWAS SNPs from ImmunoBase
# ## a) provide input data
# data.file <- "http://galahad.well.ox.ac.uk/bigdata/ImmunoBase_GWAS.bed"
# 
# ## b) perform enrichment analysis using FANTOM expressed enhancers
# eTerm <- xGRviaGenomicAnnoAdv(data.file=data.file, format.file="bed",
# GR.annotation="FANTOM5_Enhancer_Cell", num.samples=1000, gap.max=50000,
# RData.location=RData.location)
# 
# ## c) view enrichment results for the top significant terms
# xEnrichViewer(eTerm)
# 
# ## d) barplot of enriched terms
# bp <- xEnrichBarplot(eTerm, top_num='auto', displayBy="fdr")
# bp
# 
# ## e) save enrichment results to the file called 'Regions_enrichments.txt'
# output <- xEnrichViewer(eTerm, top_num=length(eTerm$adjp),
# sortBy="adjp", details=TRUE)
# utils::write.table(output, file="Regions_enrichments.txt", sep="\t",
# row.names=FALSE)
# ## End(Not run)

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Description

Usage

Arguments

Value

See Also

Examples