pseudoMA: Make a 'pseudo' MA plot Make a MA plot even when you have...

In kevincjnixon/BinfTools: Useful functions for standard analyses

Make a 'pseudo' MA plot Make a MA plot even when you have only n=1. Note that this can be used if one or both condition groups have more than one or more replicates.

Description

Make a 'pseudo' MA plot Make a MA plot even when you have only n=1. Note that this can be used if one or both condition groups have more than one or more replicates.

Usage

pseudoMA(
  counts,
  treat,
  con,
  FoldChange = 1,
  title = "",
  retDA = FALSE,
  retRes = FALSE
)

Arguments

counts	data frame of normalized counts to be used.
treat	character vector of column name(s) in counts to be used as the treatment condition.
con	character vector of column name(s) in counts to be used as the control/reference condition.
FoldChange	absolute log2FoldChange threshold (treat/con) to subset the 'differently activated' genes - Note no statistics are performed with this, and so these genes cannot be named as 'differential'
title	Character indicating the title of the plot
retDA	Boolean indicating if differently activated genes should be returned as a list (Down, Up). Default is FALSE.
retRes	Boolean indicating if 'pseudo' results object should be returned. Default is FALSE, and will not return if retDA=TRUE. Note that any p-values indicated in this table are dummy values.

Value

MA plot with differently activated genes highlighted, named list of differently activated genes if retDA=TRUE, and 'pseudo' results object if retRes=TRUE (and retDA=FALSE).

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.