get_abundant_genes: Find the set of most/least abundant genes according to limma...

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

Find the set of most/least abundant genes according to limma and friends following a differential expression analysis.

Description

Given a data set provided by limma, deseq, edger, etc; one might want to know what are the most and least abundant genes, much like get_sig_genes() does to find the most significantly different genes for each contrast.

Usage

get_abundant_genes(
  datum,
  type = "limma",
  n = NULL,
  z = NULL,
  fx = "mean",
  unique = FALSE
)

Arguments

datum	Output from the _pairwise() functions.
type	Extract abundant genes according to what?
n	Perhaps take just the top/bottom n genes.
z	Or take genes past a given z-score.
fx	Choose a function when choosing the most abundant genes.
unique	Unimplemented: take only the genes unique among the conditions surveyed.

Value

List of data frames containing the genes of interest.

See Also

[get_sig_genes()]

Examples

## Not run: 
 abundant <- get_abundant_genes(all_pairwise_output, type = "deseq", n = 100)
 ## Top 100 most abundant genes from deseq
 least <- get_abundant_genes(all_pairwise_output, type = "deseq", n = 100, least = TRUE)
 ## Top 100 least abundant genes from deseq
 abundant <- get_abundant_genes(all_pairwise_output, type = "edger", z = 1.5)
 ## Get the genes more than 1.5 standard deviations from the mean.

## End(Not run)

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