preprocessReads {systemPipeR} | R Documentation |
Applies custom read preprocessing functions to single-end or paired-end FASTQ
files. The function uses the FastqStreamer
function from the ShortRead
package to stream through large files in a memory-efficient manner.
preprocessReads(args, Fct, batchsize = 1e+05, overwrite = TRUE, ...)
args |
Object of class |
Fct |
|
batchsize |
Number of reads to process in each iteration by the internally used |
overwrite |
If |
... |
To pass on additional arguments to the internally used |
Writes to files in FASTQ format. Their names are specified by outpaths(args)
.
Thomas Girke
FastqStreamer
## Preprocessing of single-end reads param <- system.file("extdata", "trim.param", package="systemPipeR") targets <- system.file("extdata", "targets.txt", package="systemPipeR") args <- systemArgs(sysma=param, mytargets=targets) ## Not run: preprocessReads(args=args, Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE) ## End(Not run) ## Preprocessing of paired-end reads param <- system.file("extdata", "trimPE.param", package="systemPipeR") targets <- system.file("extdata", "targetsPE.txt", package="systemPipeR") args <- systemArgs(sysma=param, mytargets=targets) ## Not run: preprocessReads(args=args, Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE) ## End(Not run)