plotKnockdown: Plot gene expression with knockdown efficiency

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Plot gene expression with knockdown efficiency

Description

Plot gene expression with knockdown efficiency

Usage

plotKnockdown(
  goiExpr,
  exprsVar = "exprs",
  groupVar = "group",
  controlGroup = NULL,
  trans = "identity",
  exprsUnit = "Arbitrary Unit",
  test = c("wilcox.test", "t.test")
)

Arguments

goiExpr	A data.frame containing expression of gene of interest in linear scale, which must contain columns given below as exprsVar and groupVar.
exprsVar	Character, the variable name of expression. The unit must be in linear scale, not in logarithmic scale, otherwise the knockdown efficiency calculation will be wrong.
groupVar	Character, the variable name of grouping. The column must be a factor or a character.
controlGroup	NULL or character. If groupVar is a factor and controlGroup is NULL, then the first level is assumed to be the control. Otherwise, controlGroup must be in the group variable.
trans	Character, transformation of the y-axis, commonly used values include identity (do not transform), log10, and log2.
exprsUnit	Character, unit name of expression (TPM, CPM, RPKM, etc.)
test	Character, statistical test, wilcox.test and t.test are supported.

Examples

myData <- data.frame(group=gl(3,4),
 exprs=as.vector(sapply(c(100, 10, 1), function(x) rnorm(4, x))))
plotKnockdown(myData)

myData2 <-  data.frame(group=rep(c("Vehicle", "Dose1", "Dose2"), each=4),
 exprs=as.vector(sapply(c(100, 10, 1), function(x) rnorm(4, x))))
plotKnockdown(myData2, controlGroup="Vehicle")

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.