compare_de_results: Compare the results of separate all_pairwise() invocations.

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

Compare the results of separate all_pairwise() invocations.

Description

Where compare_led_tables looks for changes between limma and friends, this function looks for differences/similarities across the models/surrogates/etc across invocations of limma/deseq/edger.

Usage

compare_de_results(
  first,
  second,
  cor_method = "pearson",
  try_methods = c("limma", "deseq", "edger")
)

Arguments

first	One invocation of combine_de_tables to examine.
second	A second invocation of combine_de_tables to examine.
cor_method	Method to use for cor.test().
try_methods	List of methods to attempt comparing.

Details

Tested in 29de_shared.R

Value

A list of compared columns, tables, and methods.

See Also

[all_pairwise()]

Examples

## Not run: 
 first <- all_pairwise(expt, model_batch = FALSE, excel = "first.xlsx")
 second <- all_pairwise(expt, model_batch = "svaseq", excel = "second.xlsx")
 comparison <- compare_de_results(first$combined, second$combined)

## End(Not run)

elsayed-lab/hpgltools documentation built on April 8, 2024, 1:30 a.m.