Read the transcript groups that Terminus builds

Terminus groups the transcripts whose abundances the reads cannot estimate separately and reports one consensus grouping for a set of samples. Run it on Salmon output made with --numGibbsSamples (or --numBootstraps), --dumpEq and --dumpEqWeights:

Usage

read_terminus_groups(path, ignore_after_bar = TRUE)

Arguments

path

The clusters.txt file, or a folder that holds it (the output folder of one sample, or the folder given to -o when it holds one sample folder).

ignore_after_bar

Logical. Keep only the part of transcript names before the first |.

Value

A tibble with group_id, transcript_id and group_size.

Details

terminus group -d quant/sample1 -o terminus/out
terminus collapse -d quant/sample1 quant/sample2 -o terminus/out

collapse writes clusters.txt in the output folder of every sample: one line per group, the name of the group followed by its transcripts, separated by commas. read_terminus_groups() reads that file into a long table that add_uncertainty() accepts in its groups argument, so that the groups of Terminus replace the groups built from the correlation of the replicates.

See also

add_uncertainty(), isoform_ambiguity()

Examples

clusters <- tempfile(fileext = ".txt")
writeLines(
  c(
    "NewTr1,ENST00000831217.1,ENST00000831165.1",
    "NewTr2,ENST00000831423.1,ENST00000831157.1,ENST00000831246.1"
  ),
  clusters
)
read_terminus_groups(clusters)
#> # A tibble: 5 × 3
#>   group_id transcript_id     group_size
#>   <chr>    <chr>                  <int>
#> 1 NewTr1   ENST00000831217.1          2
#> 2 NewTr1   ENST00000831165.1          2
#> 3 NewTr2   ENST00000831423.1          3
#> 4 NewTr2   ENST00000831157.1          3
#> 5 NewTr2   ENST00000831246.1          3