preprocessReads {systemPipeR} | R Documentation

## Run custom read preprocessing functions

### Description

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.

### Usage

    preprocessReads(args, Fct, batchsize = 1e+05, overwrite = TRUE, ...)

### Arguments

`args` | Object of class `SYSargs` or `SYSargs2`.
`Fct` | `character` string of custom read preprocessing function call where both the input and output needs to be an object of class `ShortReadQ`. The name of the input `ShortReadQ` object needs to be `fq`.
`batchsize` | Number of reads to process in each iteration by the internally used `FastqStreamer` function.
`overwrite` | If `TRUE` existing file will be overwritten.
`...` | To pass on additional arguments to the internally used `writeFastq` function.

### Value

Writes to files in FASTQ format. Their names are specified by `outpaths(args)`.

### Author(s)

Thomas Girke

### See Also

FastqStreamer

### Examples

    ## 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)

[Package systemPipeR version 1.22.0 Index]