ebseq_pairwise_subset: Perform pairwise comparisons with ebseq, one at a time.

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

Perform pairwise comparisons with ebseq, one at a time.

Description

This uses the same logic as in the various *_pairwise functions to invoke the 'normal' ebseq pairwise comparison for each pair of conditions in an expressionset. It therefore avoids the strange logic inherent in the ebseq multitest function.

Usage

ebseq_pairwise_subset(
  input,
  ng_vector = NULL,
  rounds = 10,
  target_fdr = 0.05,
  model_batch = FALSE,
  model_cond = TRUE,
  model_intercept = FALSE,
  alt_model = NULL,
  keepers = NULL,
  conditions = NULL,
  norm = "median",
  force = FALSE,
  ...
)

Arguments

input	Expressionset/expt to perform de upon.
ng_vector	Passed on to ebseq, I forget what this does.
rounds	Passed on to ebseq, I think it defines how many iterations to perform before return the de estimates
target_fdr	If we reach this fdr before iterating rounds times, return.
model_batch	Provided by all_pairwise() I do not think a Bayesian analysis really cares about models, but if one wished to try to add a batch factor, this would be the place to do it. It is currently ignored.
model_cond	Provided by all_pairwise(), ibid.
model_intercept	Ibid.
alt_model	Ibid.
keepers	Specify a set of contrasts to perform here.
conditions	Factor of conditions in the data, used to define the contrasts.
norm	EBseq normalization method to apply to the data.
force	Flag used to force inappropriate data into the various methods.
...	Extra arguments passed downstream, noably to choose_model()

Value

A pairwise comparison of the various conditions in the data.

See Also

[ebseq_pairwise()]

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