calculate_DTU: Set up and execute the tests.

View source: R/func.R

calculate_DTUR 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)

Value

list


bartongroup/RATS documentation built on June 8, 2022, 12:40 a.m.