combineAnnotatePeaks: Combine and annotate peaks from different sample types....

In ewymathe/testALTREinstall: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

This function accomplishes three tasks: (1) Combines peaks from different sample types into one master list, and annotates each peak with it's sample type-specificity (which cell or tissue types the peak can be found in) (2) Categorizes peaks as either a promoter or enhancer (promoter distance is defined as 1500bp away from a transcription start site (TSS) by default, but the distance can be changed with the distancefromTSS argument) (3) Optionally, regulatory regions that are within a certain distance of each other can be merged to form a larger regulatory region.

Usage

combineAnnotatePeaks(conspeaks, TSS, merge = FALSE, mergedistenh = 0,
  mergedistprom = 0, mergedist = 0, regionspecific = NA,
  distancefromTSS = 1500)

Arguments

conspeaks	list of GRanges objects for each sample type (output by getConsensusPeaks() function)
TSS	file of transcription start sites
merge	whether or not regions should be merged if they are within a user set distance to each other (default is FALSE)
mergedistenh	merge enhancers peaks if they are < mergedistenh apart (set when regionspecific is TRUE)
mergedistprom	merge promoters if they are < mergedistprom apart (set when regionspecific is TRUE)
mergedist	merge promoters and enhancers if they are < mergedist apart (set when regionspecific is FALSE)
regionspecific	logical to if TRUE, merging occurs within same type peaks (e.g. merge promoters, then merge enhancers)
distancefromTSS	in bp; peaks within distFromTSS of an annotated Transcription Start Site (TSS) will be annotated as promoter (default=1500bp)

Value

List containing two items: (1) GRanges object: all sample types combined, regions annotated as type-specific and enhancer/promoter specific. (2) Matrix: number and size of enhancers and promoters before and after merging nearby regulatory regions

Examples

## Not run: 
dir <- system.file('extdata', package='ALTRE', mustWork=TRUE)
csvfile <- file.path(dir, 'lung.csv')
sampleinfo <- loadCSVFile(csvfile)
samplePeaks <- loadBedFiles(sampleinfo)
consPeaks <- getConsensusPeaks(samplepeaks=samplePeaks,minreps=2)
TSSannot <- getTSS()
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          mergedistenh = 1500,
                                          mergedistprom = 1000)

## End(Not run)

ewymathe/testALTREinstall documentation built on May 16, 2019, 9:42 a.m.