import-bam {AllelicImbalance} | R Documentation

## Import Bam

### Description

Imports a specified genomic region from a bam file using a GRanges object as search area.

### Usage

    impBamGAL(UserDir, ...)

    ## S4 method for signature 'character'
    impBamGAL(
      UserDir,
      searchArea,
      files = NULL,
      XStag = FALSE,
      verbose = TRUE,
      ...
    )

### Arguments

`UserDir` | The relative or full path of folder containing bam files.
`...` | arguments to pass on
`searchArea` | A `GenomicRanges object` that contains the regions of interest
`files` | use character vector to specify one or more files to import. The default imports all bam files from the directory.
`XStag` | Setting `XStag=TRUE` stores the strand specific information in the mcols slot 'XS'
`verbose` | makes the function more talkative.

### Details

If the sequence data is strand-specific you may want to set XStag=TRUE. The strand specific information has then to be stored in the meta columns with column name 'XS'. If the aligner did not set the XS-tag and the data is strand- specific it is still be possible to infer the strand from the bit flags after importing the reads to R. Depending on the strand-specific protocol different combinations of the flags will have to be used. For illumina fr-secondstrand, 83 and 163 are minus strand reads and 99 and 147 are plus strand reads.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    #Declare searchArea
    searchArea <- GRanges(seqnames=c('17'), ranges=IRanges(79478301,79478361))

    #Relative or full path
    pathToFiles <- system.file('extdata/ERP000101_subset', package='AllelicImbalance')

    #all files in directory
    reads <- impBamGAL(pathToFiles,searchArea,verbose=FALSE)
    #specified files in directory
    reads <- impBamGAL(pathToFiles,searchArea,
    			files=c("ERR009160.bam", "ERR009167.bam"),verbose=FALSE)

[Package AllelicImbalance version 1.32.0 Index]