GREP2 (version 1.0.2)

run_tximport: Wrapper function to run tximport

Description

run_tximport function runs tximport on transcript level abundances from Salmon to summarize to gene level. See Bioconductor package tximport for details.

Usage

run_tximport(srr_id, species = c("human", "mouse", "rat"), salmon_dir,
  countsFromAbundance = c("no", "scaledTPM", "lengthScaledTPM"))

Arguments

srr_id

SRA run accession ID.

species

name of the species. Only 'human', 'mouse', and 'rat' are allowed to use.

salmon_dir

directory where salmon files are saved. This should be the folder created by Salmon and is called "salmon".

countsFromAbundance

whether to generate counts based on abundance. Available options are: 'no', 'scaledTPM' (abundance based estimated counts scaled up to library size), 'lengthScaledTPM' (default, scaled using the average transcript length over samples and library size).

Value

a list of gene and transcript level estimated counts.

Details

We use Ensembl annotation for both genes and transcripts.

References

Charlotte Soneson, Michael I. Love, Mark D. Robinson (2015): Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research. http://dx.doi.org/10.12688/f1000research.7563.1

Examples

# NOT RUN {
#Run this function after running Salmon.
salmon_dir=system.file("extdata","", package="GREP2")
run_tximport(srr_id="SRR5890521", species="human",
salmon_dir=salmon_dir,countsFromAbundance="lengthScaledTPM")

# }