ezMethodSubsampleReads: Subsample reads in a fastq dataset file

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

Subsample reads in a fastq dataset file

Description

The subsampled reads are equally distributed across the original files

Usage

  ezMethodSubsampleReads(input = NA, output = NA, param = NA)

Arguments

param

a list of parameters where the following entries are used dataRoot the prefix of the file paths nReads the number of reads to keep; if given will be used to compute subsampleFactor; it is not guaranteed that the number of reads kept is exact subsampleFactor the factor by which subsampling has been done. if nReads is specified subsampleFactor will not be used paired whether these are paired-end reads

Examples

  inputDatasetFile = system.file(package = "ezRun", "extdata/yeast_10k/dataset.tsv")
  param = ezParam(list(dataRoot=system.file(package = "ezRun"), nReads=100))
  input = EzDataset(file=inputDatasetFile, dataRoot=param$dataRoot)
  xSubsampled = ezMethodSubsampleReads(input=input, param=param)
  file.remove(xSubsampled$getFullPaths("Read1"))

uzh/ezRun documentation built on April 14, 2024, 5:09 a.m.