run_tximport: Wrapper function to run tximport
In anilchalisey/rseqR: RNA-seq data processing pipeline

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.

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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 `'human'`, and `'mouse'` are supported at present. [DEFAULT = human].
`salmon.files`	character vector specifying path to quant.sf files.
`summarise`	logical, if `TRUE` then return gene-level summary, otherwise return transcript level data.
`countsFromAbundance`	whether to generate counts based on abundance. Available options are: `'no'`, `'scaledTPM'` (abundance based estimated counts scaled up to library size), `'lengthScaledTPM'`.

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

anilchalisey/rseqR documentation built on May 25, 2019, 2:25 p.m.