import-bam: Import Bam

In AllelicImbalance: Investigates Allele Specific Expression

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)

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.