run_kallisto_bulk: Runs kallisto quantification for bulk samples.

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

Runs kallisto quantification for bulk samples.

Description

For pair-ended experiments, reads for each pair should be in a seperate file.

Usage

run_kallisto_bulk(
  indices_dir,
  data_dir,
  quant_meta = NULL,
  paired = NULL,
  species = "homo_sapiens",
  release = "94",
  fl.mean = NULL,
  fl.sd = NULL,
  ncores = 1,
  updateProgress = NULL
)

Arguments

indices_dir	Directory with kallisto indices. See build_kallisto_index.
data_dir	Directory with raw fastq.gz RNA-Seq files.
quant_meta	Previous result of get_quant_meta (for fastqs downloaded by 'GEOfastq') or select_pairs (for non-public fastqs). Must contain column 'File Name' and optionally 'Pair' (rows with same value taken as paired), and Replicate (rows with same valued taken as replicates). quant_meta is used to bypass call to select_pairs GUI.
paired	Boolean indicating if fastq files are paired. If NULL (default), fastqs are considered paired if they are non NA entries in quant_meta$Pair.
species	Species name. Default is homo_sapiens. Used to determine transcriptome index to use.
release	Character vector of EnsDB release number. Release '94' is the default because HGNC symbols most closely overlap with those used to annotate CMAP02 and L1000.
fl.mean	Estimated average fragment length (only relevant for single-end reads). Default (NULL) uses 200.
fl.sd	Estimated standard deviation of fragment length (only relevant for single-end reads). Default (NULL) uses 20.
ncores	Number of cores to run quantification with. Default is 1.
updateProgress	Used by dseqr app to provide visual update of progress.

Value

Called for side effects. Saves result of 'kallisto' quantification.

alexvpickering/rkal documentation built on Nov. 27, 2022, 8:38 p.m.