filterFastqByBam: Filters FastQ files by bam

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Filters FastQ files by bam

Description

Filters FastQ files by bam and writes them into new files.

Usage

filterFastqByBam(
  fqFiles,
  bamFile,
  fqOutFiles = NULL,
  doGzip = TRUE,
  keepUnmapped = TRUE,
  isProperPair = NA
)

removeReadsFromFastq(fqFiles, readIds, fqOutFiles = NULL, doGzip = TRUE)

Arguments

fqFiles	a character vector representing file paths to FastQ files.
bamFile	a character representing the bam file path.
fqOutFiles	an optional character vector representing file paths to the FastQ output files.
doGzip	a logical indicating whether to archive the output files in a gzip archive.
keepUnmapped	passed further to scanBamFlag().
isProperPair	passed further to scanBamFlag().
readIds	a character containing the read ID's from the bamFile.

Value

Returns the names of the filtered FastQ files.

Functions

• removeReadsFromFastq: Removes reads from the FastQ files according to the bam filter.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

scanBam

ScanBamParam

Examples

bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)
file = system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE)
param = list()
param$dataRoot = system.file(package="ezRun", mustWork = TRUE)
input = EzDataset$new(file=file, dataRoot=param$dataRoot)
fqFiles = input$getFullPaths("Read1")
fqFiltered = filterFastqByBam(fqFiles, bamFile, doGzip = FALSE)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.