countFinalRegions: countFinalRegions

In drighelli/DEScan2: Differential Enrichment Scan 2

countFinalRegions

Description

count reads falling within the final regions.

Usage

countFinalRegions(
  regionsGRanges,
  readsFilePath = NULL,
  fileType = c("bam", "bed"),
  minCarriers = 2,
  genomeName = NULL,
  onlyStdChrs = FALSE,
  carrierscolname = "k-carriers",
  ignStrandSO = TRUE,
  modeSO = "Union",
  saveFlag = FALSE,
  savePath = "finalRegions",
  verbose = TRUE
)

Arguments

regionsGRanges	a GRanges objects representing the peaks to compute the coverage, with a "k-carriers" mcols. (tipically generated by finalRegions function).
readsFilePath	the filepath of bam or bed files necessary to compute the coverage.
fileType	the file type of the input files.
minCarriers	minimum number of carriers (samples).
genomeName	code name of the genome of reads files (i.e. "mm9").
onlyStdChrs	a flag indicating if to keep only the standard chromosomes
carrierscolname	character describing the name of the column within the carriers number (default is "k-carriers").
ignStrandSO	a flag indicating if to ignore the reads strand. (see GenomicAlignments::summarizeOverlaps).
modeSO	the mode to use, default is "Union". (see GenomicAlignments::summarizeOverlaps).
saveFlag	a flag indicating if to save the results.
savePath	the path where to store the results.
verbose	verbose output.

Value

A SummarizedExperiment object containing as assays the read counts matrix with regions as rows and samples as columns, and as rowRanges the GRanges object representing the peaks used as rows in the matrix.

Examples

filename <- system.file("extdata/regions/regions.rds", package="DEScan2")
regionsGR <- readRDS(file=filename)
reads.path <- system.file("extdata/bam", package="DEScan2")
finalRegionsSE <- countFinalRegions(regionsGRanges=regionsGR,
    readsFilePath=reads.path, fileType="bam", minCarriers=1,
    genomeName="mm9", onlyStdChrs=TRUE, ignStrandSO=TRUE, saveFlag=FALSE,
    verbose=TRUE)
library("SummarizedExperiment")
assay(finalRegionsSE) ## matrix of counts
rowRanges(finalRegionsSE) ## the GRanges of the input regions

drighelli/DEScan2 documentation built on March 21, 2023, 3:06 p.m.