import_quants: Import kallisto quants

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

Import kallisto quants

Description

Import kallisto quants

Usage

import_quants(data_dir, species = "Homo sapiens", release = "94")

Arguments

data_dir	Directory with raw and quantified RNA-Seq files.
species	The species. Default is 'homo_sapiens'.
release	ensembl release. Default is 94 (latest in release for AnnotationHub - needs to match with build_ensdb).

Value

list with items

• quantsDGEList from tximport with argument countsFromAbundance = 'lengthScaledTPM'

• txi.deseqDGEListfrom tximport with argument countsFromAbundance = 'no'

Examples

library(tximportData)
example <- system.file("extdata", "kallisto_boot",
    "ERR188021",
    package = "tximportData"
)

# setup to mirror expected folder structure
data_dir <- tempdir()
qdir <- paste("kallisto", get_pkg_version(), "quants", sep = "_")
qdir <- file.path(data_dir, qdir)
unlink(qdir, recursive = TRUE)
dir.create(qdir)
file.copy(example, qdir, recursive = TRUE)
quants <- import_quants(data_dir)

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