kallistoQuant: Kallisto quantifies transcript abundance from RNA-Seq data.

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

The data is broken down into k-mers and each k-mer is pseudoaligned to k-mers in the index. Because kallisto doesn't rely on full alignment, it is much quicker than other methods, without losing accuracy.

Usage

kallistoQuant(dataFile, preFilt = FALSE, refIndex,
  refIndexFromPackage = FALSE, bootstrap = 0, fragmentLength = 200,
  fragmentSD = 10, biasCor = FALSE)

Arguments

refIndex	A character string of the name of the index file (usually, .idx) against which the fastq files are pseudoaligned. This file can be generated from a fasta-formatted transcriptome file using kallistoIndex.
refIndexFromPackage	A logical, false by default. If the user would like to use an index provided by the package (these can be viewed using availableReferences(), he/she should specifiy "true" here. Otherwise, the function will assume the index is provided by the user.
bootstrap	An integer specifying the number of times to bootstrap. The output will provide a measure of variance.
fragmentLength	An integer. Estimated fragment length. Only required for single-end data (for paired-end data, Kallisto is able to calculate the fragment length). Default is 200 bp.
fragmentSD	A numeric. The standard deviation of the fragment length. Only required for single-end data (for paired-end data, Kallisto is able to calculate the standard deviation). Default is 10 bp.
file1	A character string of the name of the RNA-Seq data file (fastq.gz) to be processed.
file2	A character string of the RNA-Seq data file (fastq.gz) to be processed - in the case there is paired-end data.
pairedEnd	is a logical. If true (default), a paired end protocol is chosen (for this, the file1 and file2 parameters must be specified). If false, a single end protocol will be run, and only file1 will be processed.

Value

A data frame of the estimated abundances of each transcript specified in the input file(s). The data frame is also saved to a folder, which is given the title of the files, exlcuding the extensions. The folder contains these abundances (in text format and compressed format), as well as information about the run.

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.