import_kallisto: Import quantifications from Kallisto

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

Import quantifications from Kallisto

Description

Import quantifications from Kallisto

Usage

import_kallisto(filenames, anno, txOut = FALSE, ignoreTxVersion = FALSE)

Arguments

filenames	Paths to the abundance files.
anno	The filename for the annotation in csv (see anno package) It must have the following columns: id, ensembl_gene, symbol, entrez_id and transcript_type. Values can be NA except for id and ensembl_gene.
txOut	Return counts and abundance at the transcript level. Default: FALSE
ignoreTxVersion	Ignore version of tx. Default = FALSE

Value

A txi object.

Examples

abundances <- get_demo_abundance_files()
file_anno <- get_demo_anno_file()
txi <- import_kallisto(abundances, anno = file_anno)

CharlesJB/rnaseq documentation built on Oct. 17, 2023, 5:37 p.m.