get_sig_genes: Get a set of up/down differentially expressed genes.

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

Get a set of up/down differentially expressed genes.

Description

Take one or more criteria (fold change, rank order, (adj)p-value, z-score from median FC) and use them to extract the set of genes which are defined as 'differentially expressed.' If no criteria are provided, it arbitrarily chooses all genes outside of 1-z.

Usage

get_sig_genes(
  table,
  n = NULL,
  z = NULL,
  lfc = NULL,
  p = NULL,
  min_mean_exprs = NULL,
  exprs_column = "deseq_basemean",
  column = "logFC",
  fold = "plusminus",
  p_column = "adj.P.Val",
  comparison = "orequal"
)

Arguments

table	Table from limma/edger/deseq.
n	Rank-order top/bottom number of genes to take.
z	Number of z-scores >/< the median to take.
lfc	Fold-change cutoff.
p	P-value cutoff.
min_mean_exprs	Exclude genes with less than this mean expression.
exprs_column	Use this column for filtering by expression.
column	Table's column used to distinguish top vs. bottom.
fold	Identifier reminding how to get the bottom portion of a fold-change (plusminus says to get the negative of the positive, otherwise 1/positive is taken). This effectively tells me if this is a log fold change or not.
p_column	Table's column containing (adjusted or not)p-values.
comparison	When set to orequal, use >=/<= instead of jsut >/<.

Value

Subset of the up/down genes given the provided criteria.

See Also

[extract_significant_genes()] [get_abundant_genes()]

Examples

## Not run: 
 sig_table <- get_sig_genes(table, lfc = 1)

## End(Not run)

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