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
gene will be discarded. To save a file with those columns,
directly save the transcript to gene data frame with function like
save_tr2g_bustools(tr2g, file_save = "./tr2g.tsv")
The data frame output from the
File name of the file to be saved. The directory in which the file is to be saved must exist.
Nothing is returned into the R session. A tsv file of the format
bustools with the name and directory specified will be written
This function has been superseded by the new version of tr2g_* functions that can extract transcriptome for only the biotypes specified and with only the standard chromosomes. The new version of tr2g_* functions also sorts the transcriptome so the tr2g and the transcriptome have transcripts in the same order, and write the tr2g.tsv file in the bustools format.
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toy_path <- system.file("testdata", package = "BUSpaRse") file_use <- paste(toy_path, "gtf_test.gtf", sep = "/") tr2g <- tr2g_gtf(file = file_use, get_transcriptome = FALSE, write_tr2g = FALSE, save_filtered_gtf = FALSE) save_tr2g_bustools(tr2g, file_save = "./tr2g.tsv") # Clean up files from the example file.remove("tr2g.tsv")
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