plotSSGS: plot SSGS gene classes

In RNAsense: Analysis of Time-Resolved RNA-Seq Data

Description

Genes are sorted into groups with respect to switch time and time point of fold change detection. For each group, results of wild type and knockdown-condition are compared by means of fisher's exact test to show whether the knocked down gene enhances or suppresses the respective gene group.

Usage

plotSSGS(myresultCombined = resultCombined, mytimes = times,
  myanalyzeConditions = analyzeConditions)

Arguments

myresultCombined	data.frame, output of combineResults
mytimes	Numeric vector, Time points of the time-resolved RNA-seq data
myanalyzeConditions	character vector, the conditions that were analyzed

Value

SSGS color plot in ggplot format

Author(s)

Marcus Rosenblatt, [e-mail]

Examples

library(ggplot2)
data(MZsox)
mydata <- MZsox[seq(1,nrow(MZsox), by=10),]
resultFC <- getFC(dataset = mydata,
myanalyzeConditions = c("WT", "MZsox"),
cores = 1,
mytimes = c(2.5,3,3.5,4,4.5,5,5.5,6))
resultSwitch <- getSwitch(dataset = mydata,
experimentStepDetection = "WT",
cores = 1,
mytimes = c(2.5,3,3.5,4,4.5,5,5.5,6))
resultCombined <- combineResults(resultSwitch, resultFC)
plotSSGS(myresultCombined = resultCombined,
mytimes = c(2.5,3,3.5,4,4.5,5,5.5,6),
myanalyzeConditions = c("WT", "MZsox"))

RNAsense documentation built on Nov. 8, 2020, 5:07 p.m.