basic_pairwise: The simplest possible differential expression method.

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

The simplest possible differential expression method.

Description

Perform a pairwise comparison among conditions which takes nothing into account. It _only_ takes the conditions, a mean value/variance among them, divides by condition, and returns the result. No fancy nomalizations, no statistical models, no nothing. It should be the very worst method possible. But, it should also provide a baseline to compare the other tools against, they should all do better than this, always.

Usage

basic_pairwise(
  input = NULL,
  design = NULL,
  conditions = NULL,
  batches = NULL,
  model_cond = TRUE,
  model_intercept = FALSE,
  alt_model = NULL,
  model_batch = FALSE,
  force = FALSE,
  keepers = NULL,
  fx = "mean",
  ...
)

Arguments

input	Count table by sample.
design	Data frame of samples and conditions.
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()
force	Force as input non-normalized data?
keepers	Set of specific contrasts to perform instead of all.
fx	What function to use for mean/median?
...	Extra options passed to arglist.

Details

Tested in test_27de_basic.R This function was written after the corresponding functions in de_deseq.R, de_edger.R, and de_limma.R. Like those, it performs the full set of pairwise comparisons and returns a list of the results. As mentioned above, unlike those, it is purposefully stupid.

Value

Df of pseudo-logFC, p-values, numerators, and denominators.

See Also

[deseq_pairwise()] [limma_pairwise()] [edger_pairwise()] [ebseq_pairwise()]

Examples

## Not run: 
 expt <- create_expt(metadata = "sample_sheet.xlsx", gene_info = "annotations")
 basic_de <- basic_pairwise(expt)
 basic_tables <- combine_de_tables(basic_de)

## End(Not run)

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