sort_tr2g {BUSpaRse} | R Documentation

## Sort transcripts to the same order as in kallisto index

### Description

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 `bus` file. Sorting is vital to obtain the correct sparse matrix from the `bus` file as equivalence class notations are based on the index of transcripts in the kallisto index.

### Usage

    sort_tr2g(tr2g, file, kallisto_out_path)

### Arguments

`tr2g` | The data frame output from the `tr2g_*` family of functions.
`file` | Character vector of length 1, path to a tsv file with transcript IDs and the corresponding gene IDs, in the format required for `bustools`, or written by `save_tr2g_bustools`.
`kallisto_out_path` | Character vector of length 1, path to the directory for the outputs of kallisto bus.

### Details

Since the attribute field of GTF and GFF3 files varies across sources, output from `tr2g_gtf` and `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 `transcript`

### Value

A data frame with columns `transcript` and `gene` and the other columns present in `tr2g` or the data frame in `file`, with the transcript IDs sorted to be in the same order as in the kallisto index.

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This function has been superseded by the new version of tr2g_* functions that can extract transcriptome for only the biotypes specified and with only the standard chromosomes.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

### See Also

Other functions to retrieve transcript and gene info: `tr2g_EnsDb()`, `tr2g_TxDb()`, `tr2g_ensembl()`, `tr2g_fasta()`, `tr2g_gff3()`, `tr2g_gtf()`, `transcript2gene()`

### 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, transcript_version = NULL)
    tr2g <- sort_tr2g(tr2g, kallisto_out_path = toy_path)

[Package BUSpaRse version 1.4.2 Index]