save_tr2g_bustools: Save transcript to gene file for use in 'bustools'

In lambdamoses/BUStoolsR: kallisto | bustools R utilities

Save transcript to gene file for use in bustools

Description

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.

Usage

save_tr2g_bustools(tr2g, file_save = "./tr2g.tsv")

Arguments

tr2g	The data frame output from the tr2g_* family of functions.
file_save	File name of the file to be saved. The directory in which the file is to be saved must exist.

Value

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.

Note

This function has been superseded by the new version of tr2g_* functions that can extract transcriptome for only the biotypes specified and with only the standard chromosomes.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.

Examples

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")

lambdamoses/BUStoolsR documentation built on Aug. 1, 2024, 6:30 a.m.