calculate_DTU: Set up and execute the tests.
In bartongroup/RATS: Relative Abundance of Transcripts

calculate_DTU

R Documentation

Set up and execute the tests.

Description

Set up and execute the tests.

Usage

calculate_DTU(
  counts_A,
  counts_B,
  tx_filter,
  test_transc,
  test_genes,
  full,
  count_thresh,
  p_thresh,
  dprop_thresh,
  correction,
  threads = 1,
  use_sums = FALSE
)

Arguments

`counts_A`	A data.table of counts for condition A. x: sample, y: transcript.
`counts_B`	A data.table of counts for condition B. x: sample, y: transcript.
`tx_filter`	A data.table with target_id and parent_id. Pre-processed with `tidy_annot()`.
`test_transc`	Whether to do transcript-level test.
`test_genes`	Whether to do gene-level test.
`full`	Either "full" (for complete output structure) or "short" (for bootstrapping).
`count_thresh`	Minimum average count across replicates.
`p_thresh`	The p-value threshold.
`dprop_thresh`	Minimum difference in proportions.
`correction`	Multiple testing correction type.
`threads`	Number of threads (POSIX systems only).
`use_sums`	Use sums instead of means. (sums is the behaviour of RATs up to 0.6.5 inclusive, more sensitivie but more prone to false positives)