plot_num_siggenes: Given a DE table with fold changes and p-values, show how...

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

Given a DE table with fold changes and p-values, show how 'significant' changes with changing cutoffs.

Description

Sometimes one might want to know how many genes are deemed significant while shifting the bars which define significant. This provides that metrics as a set of tables of numbers of significant up/down genes when p-value is held constant, as well as number when fold-change is held constant.

Usage

plot_num_siggenes(
  table,
  methods = c("limma", "edger", "deseq", "ebseq"),
  bins = 100,
  constant_p = 0.05,
  constant_fc = 0
)

Arguments

table	DE table to examine.
methods	List of methods to use when plotting.
bins	Number of incremental changes in p-value/FC to examine.
constant_p	When plotting changing FC, where should the p-value be held?
constant_fc	When plotting changing p, where should the FC be held?

Value

Plots and dataframes describing the changing definition of 'significant.'

See Also

[ggplot2]

Examples

## Not run: 
 pairwise_result <- all_pairwise(expt)
 crazy_sigplots <- plot_num_siggenes(pairwise_result)

## End(Not run)

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