getSwitch: Detect switching genes

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

Description

For each gene, time-resolved RNA-seq measurements are analyzed for occurence of switches (up or down)

Usage

getSwitch(dataset = mydata, experimentStepDetection = "WT",
  pValueSwitch = 0.05, cores = 1, mytimes = times)

Arguments

dataset	Object of class SummarizedExperiment, output of SummarizedExperiment, as assays use a numeric matrix with your RNAseq count data, rows correspond to different genes, columns correspond to different experiments, as rowData provide a DataFrame with columns name (geneID) and genename (the gene names), as colData provide a DataFrame with columns condition, time and replicate
experimentStepDetection	Character, Name of condition for which switch detection is performed
pValueSwitch	Numeric, pValue for switch detection
cores	Numeric, Number of cores for parallelization, default 1 for no parallelization
mytimes	Numeric vector, Time points of the time-resolved RNA-seq data

Value

Data.frame containing gene names and results of switch detection, information about switch time point and direction

Author(s)

Marcus Rosenblatt, [e-mail]

Examples

data(MZsox)
mydata <- MZsox[seq(1,nrow(MZsox), by=20),]
resultSwitch <- getSwitch(dataset = mydata,
experimentStepDetection = "WT",
cores = 1,
mytimes = c(2.5,3,3.5,4,4.5,5,5.5,6))

marcusrosenblatt/RNAsense documentation built on Dec. 7, 2020, 5:26 p.m.