Description Usage Arguments Details Value References Examples
run_tximport
function runs tximport on transcript level
abundances from Salmon to summarize to gene level. See Bioconductor
package tximport for details.
1 2 | run_tximport(srr_id, species = c("human", "mouse", "rat"), salmon_dir,
countsFromAbundance = c("no", "scaledTPM", "lengthScaledTPM"))
|
srr_id |
SRA run accession ID. |
species |
name of the species. Only |
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: |
We use Ensembl annotation for both genes and transcripts.
a list of gene and transcript level estimated counts.
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
1 2 3 4 | #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")
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