save_tr2g_bustools {BUSpaRse} | R Documentation |
bustools
This function saves the transcript to gene data frame generated by this package
in whatever means in a format required by bustools
. In order to use
bustools
to generate the gene count or TCC matrix, a file
that maps transcripts to genes is required. This should be a tsv file with 2
columns: the first column for transcript ID and the second for gene ID. The
order of transcripts in this file must be the same as the order in the
kallisto index, and this ordering can be ensured by the function
sort_tr2g
. There must also be no headers. All columns other than
transcript
and gene
will be discarded. To save a file with those columns,
directly save the transcript to gene data frame with function like
write.table
, readr::write_delim
, and
fwrite
.
save_tr2g_bustools(tr2g, file_save = "./tr2g.tsv", ...)
tr2g |
The data frame output from the |
file_save |
File name of the file to be saved. The directory in which the file is to be saved must exist. |
... |
Other arguments passed to |
Nothing is returned into the R session. A tsv file of the format
required by bustools
with the name and directory specified will be written
to disk.
toy_path <- system.file("testdata", package = "BUSpaRse") file_use <- paste(toy_path, "gtf_test.gtf", sep = "/") tr2g <- tr2g_gtf(file = file_use, verbose = FALSE) save_tr2g_bustools(tr2g, file_save = "./tr2g.tsv")