noiseq_pairwise: Perform pairwise comparisons using noiseq.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Perform pairwise comparisons using noiseq.

Description

Perform pairwise comparisons using noiseq.

Usage

noiseq_pairwise(
  input = NULL,
  conditions = NULL,
  batches = NULL,
  model_cond = TRUE,
  model_batch = TRUE,
  annot_df = NULL,
  k = 0.5,
  norm = "rpkm",
  factor = "condition",
  lc = 1,
  r = 20,
  adj = 1.5,
  a0per = 0.9,
  filter = 1,
  keepers = NULL,
  ...
)

Arguments

input	Expressionset to compare.
conditions	Set of conditions to query
batches	known batches in the data, or a surrogate estimator.
model_cond	Add condition to the model?
model_batch	Add batch to the model, noiseq has its own combat-like method, so maybe not necessary?
annot_df	Extra annotations.
k	Taken from the noiseq docs.
norm	Normalization method (noiseq oddly defaults to rpkm).
factor	Metadata factor over which to iterate.
lc	taken from the noiseq docs.
r	taken from the noiseq docs.
adj	taken from the noiseq docs.
a0per	taken from the noiseq docs.
filter	Filter the data?
keepers	Perform the comparison only over these specific contrasts instead of all.
...	Extra arguments.

Value

List similar to deseq_pairwise/edger_pairwise/etc.

See Also

DOI:10.1093/nar/gkv711

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.