This function takes the data frame output from the
tr2g_* family of
functions in this package as the input, and sorts it so the transcripts are
in the same order as in the kallisto index used to generate the
file. Sorting is vital to obtain the correct sparse matrix from the
file as equivalence class notations are based on the index of transcripts
in the kallisto index.
sort_tr2g(tr2g, file, kallisto_out_path)
The data frame output from the
Character vector of length 1, path to a tsv file with
transcript IDs and the corresponding gene IDs, in the format required for
Character vector of length 1, path to the directory for the outputs of kallisto bus.
Since the attribute field of GTF and GFF3 files varies across sources, output
tr2g_gff3 may need further
clean up. You may also supply gene and transcript IDs from other sources.
This function should be used after the clean up, when the transcript IDs in
the cleaned up data frame have the same format as those in
A data frame with columns
gene and the
other columns present in
tr2g or the data frame in
the transcript IDs sorted to be in the same order as in the kallisto index.
This function has been superseded by the new version of tr2g_* functions that can extract transcriptome for only the biotypes specified and with only the standard chromosomes.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.
Other functions to retrieve transcript and gene info:
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, transcript_version = NULL) tr2g <- sort_tr2g(tr2g, kallisto_out_path = toy_path)
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