countFinalRegions {DEScan2} | R Documentation

## 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

[Package DEScan2 version 1.12.0 Index]