run_tximport: Wrapper function to run tximport

In GREP2: GEO RNA-Seq Experiments Processing Pipeline

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).

Details

We use Ensembl annotation for both genes and transcripts.

Value

a list of gene and transcript level estimated counts.

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

#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")

GREP2 documentation built on Sept. 3, 2019, 9:05 a.m.