pairFastqFiles: figure out how a sample's runs can be properly paired (no SE...

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

figure out how a sample's runs can be properly paired (no SE support yet)

Usage

pairFastqFiles(path = ".", extension = "\\.fastq\\.gz",
  readPrefix = "R", lanePrefix = "L", splitChar = "_", ...)

.findPairings(fragments, ...)

Arguments

path	a character string specifying where the FASTQ files are
extension	what is the file extension? default is ".fastq.gz"
readPrefix	read prefix, usually a single character, default "R"
lanePrefix	lane prefix, usually a single character, default "L"
splitChar	split character or string, usually "_" for Illumina
...	other arguments, passed on to helper functions
fragments	fragments to bind toward

Value

a vector of paired FASTQ files for runKallisto

a data.frame of paired FASTQ filenames

Functions

• .findPairings: helper function to try and weed through various possible extensions

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.