prep_expression_matrix: Prepare expression matrix of transcript- or gene-specific...

In hammerlab/rinfino: R-friendly client to run infino (http://github.com/hammerlab/infino)

Description

Prepare expression matrix of transcript- or gene-specific data given a directory containing kallisto output (one folder per sample)

Usage

prep_expression_matrix(root, output_arg, skip_missing = TRUE,
  cohort = basename(root), metric = "no", abundanceCol = "TPM",
  by = "Gene_symbol", by_gene = TRUE, suffix = "tsv",
  filename = glue::glue("abundance.{suffix}"),
  output_writer = readr::write_tsv)

Arguments

root	(chr) filepath to 'root' directory containing kallisto output
output_arg	(chr) argument to 'output_writer', typically the filename to be written
skip_missing	(bool) whether to report & ignore directories not containing output
metric	(chr) which metric to capture from kallisto. One of 'scaledTPM', 'no', (see '?tximport' for details)
by	(chr) description / name for column in output matrix containing gene or transcript
by_gene	(bool) whether to organize results by gene (TRUE) or transcript (FALSE)
suffix	(chr) file suffix to read in (either 'tsv' or 'h5' – h5 gives errors on some platforms)
filename	(chr) name of kallisto output file to ingest
output_writer	(function) function to use when saving results.

hammerlab/rinfino documentation built on May 27, 2019, 8:45 a.m.