Description Usage Arguments Details Value References
run_tximport
function runs tximport on transcript level
abundances from Salmon to summarise to gene level. See Bioconductor
package tximport for details.
1 2 3 | run_tximport(species = c("human", "mouse"), salmon.files,
summarise = TRUE, countsFromAbundance = c("no", "scaledTPM",
"lengthScaledTPM"))
|
species |
character string specifying the name of the species. Only
|
salmon.files |
character vector specifying path to quant.sf files. |
summarise |
logical, if |
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
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