correlate_de_tables: See how similar are results from limma/deseq/edger/ebseq.

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

See how similar are results from limma/deseq/edger/ebseq.

Description

limma, DEseq2, and EdgeR all make somewhat different assumptions. and choices about what makes a meaningful set of differentially. expressed genes. This seeks to provide a quick and dirty metric describing the degree to which they (dis)agree.

Usage

correlate_de_tables(results, annot_df = NULL, extra_contrasts = NULL)

Arguments

results	Data from do_pairwise()
annot_df	Include annotation data?
extra_contrasts	include some extra contrasts when comparing results.

Details

Invoked by all_pairwise().

Value

Heatmap showing how similar they are along with some correlations betwee the three players.

See Also

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

Examples

## Not run: 
 l = limma_pairwise(expt)
 d = deseq_pairwise(expt)
 e = edger_pairwise(expt)
 fun = compare_led_tables(limma = l, deseq = d, edger = e)

## End(Not run)

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