Prepare expression matrix of transcript- or gene-specific data given a directory containing kallisto output (one folder per sample)
1 2 3 4 5 | 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)
|
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. |
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