extract_abundant_genes: Extract the sets of genes which are significantly more...

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

Extract the sets of genes which are significantly more abundant than the rest.

Description

Given the output of something_pairwise(), pull out the genes for each contrast which are the most/least abundant. This is in contrast to extract_significant_genes(). That function seeks out the most changed, statistically significant genes.

Usage

extract_abundant_genes(
  pairwise,
  according_to = "deseq",
  n = 100,
  z = NULL,
  unique = FALSE,
  excel = "excel/abundant_genes.xlsx",
  ...
)

Arguments

pairwise	Output from _pairwise()().
according_to	What tool(s) define 'most?' One may use deseq, edger, limma, basic, all.
n	How many genes to pull?
z	Instead take the distribution of abundances and pull those past the given z score.
unique	One might want the subset of unique genes in the top-n which are unique in the set of available conditions. This will attempt to provide that.
excel	Excel file to write.
...	Arguments passed into arglist.

Value

The set of most/least abundant genes by contrast/tool.

See Also

openxlsx

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