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rsemverse

Read RSEM gene-level results as a table of gene symbols by samples.

Usage

Put the RSEM files in a folder and list them in metadata.csv:

metadata.csv
data/
  S1.genes.results
  S2.genes.results
sample_id,ref
S1,S1.genes.results
S2,S2.genes.results

ref is the file name inside data. Other columns are ignored.

library(rsemverse)

df <- rsem_read(
  data     = "data",
  metadata = "metadata.csv",
  species  = "human",   # "human" or "mouse"
  expr     = "tpm"      # "count" or "tpm"
)

df is a data frame: gene symbols in the rows, sample_id in the columns, in the order of metadata.csv. Save it as you like, for example write.csv(df, "tpm.csv").

What it does

  • Removes the version of Ensembl IDs (ENSG00000141510.18 → ENSG00000141510) and looks up the symbol in org.Hs.eg.db or org.Mm.eg.db.
  • Adds up the rows that end up with the same symbol.
  • Keeps a gene without a symbol under its original ID, so nothing is lost.

It stops with a message if the files do not match (missing file, different genes, wrong species, and so on). Values are not rounded or normalized. See ?rsem_read for the details.

Installation 

install.packages("BiocManager")
BiocManager::install("DaikiKumakura/rsemverse")
BiocManager::install("org.Hs.eg.db")   # human; org.Mm.eg.db for mouse

License

MIT © Daiki Kumakura