ebseq_pairwise: Set up model matrices contrasts and do pairwise comparisons...

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

Set up model matrices contrasts and do pairwise comparisons of all conditions using EBSeq.

Description

Invoking EBSeq is confusing, this should help.

Usage

ebseq_pairwise(
  input = NULL,
  patterns = NULL,
  conditions = NULL,
  batches = NULL,
  model_cond = NULL,
  model_intercept = NULL,
  alt_model = NULL,
  model_batch = NULL,
  keepers = NULL,
  ng_vector = NULL,
  rounds = 10,
  target_fdr = 0.05,
  method = "pairwise_subset",
  norm = "median",
  force = FALSE,
  ...
)

Arguments

input	Dataframe/vector or expt class containing data, normalization state, etc.
patterns	Set of expression patterns to query.
conditions	Not currently used, but passed from all_pairwise()
batches	Not currently used, but passed from all_pairwise()
model_cond	Not currently used, but passed from all_pairwise()
model_intercept	Not currently used, but passed from all_pairwise()
alt_model	Not currently used, but passed from all_pairwise()
model_batch	Not currently used, but passed from all_pairwise()
keepers	Perform a specific set of contrasts instead of all?
ng_vector	I think this is for isoform quantification, but am not yet certain.
rounds	Number of iterations for doing the multi-test
target_fdr	Definition of 'significant'
method	The default ebseq methodology is to create the set of all possible 'patterns' in the data; for data sets which are more than trivially complex, this is not tenable, so this defaults to subsetting the data into pairs of conditions.
norm	Normalization method to use.
force	Force ebseq to accept bad data (notably NA containing stuff from proteomics.
...	Extra arguments currently unused.

Value

List containing tables from ebseq, the conditions tested, and the ebseq table of conditions.

See Also

[limma_pairwise()] [deseq_pairwise()] [edger_pairwise()] [basic_pairwise()]

Examples

 ## Not run: 
  expt <- create_expt(metadata = "sample_sheet.xlsx", gene_info = annotations)
  ebseq_de <- ebseq_pairwise(input = expt)

## End(Not run)

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