detectDiffTSS: Detect differentially expressed Transcription Start Sites...

In vivekbhr/icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Detect differentially expressed Transcription Start Sites between two conditions (test)

Usage

detectDiffTSS(fit, testGroup, contGroup, TSSfile = NULL, MAplot_fdr = NA)

## S4 method for signature 'DGEGLM'
detectDiffTSS(fit, testGroup, contGroup, TSSfile = NULL, MAplot_fdr = NA)

## S4 method for signature 'DESeqDataSet'
detectDiffTSS(fit, testGroup, contGroup, MAplot_fdr = NA)

Arguments

fit	DGEGLM object (output of fitDiffTSS command )
testGroup	Test group name
contGroup	Control group name
TSSfile	The TSS .bed file used for fitDiffTSS command (if method "edgeR" was used)
MAplot_fdr	FDR threshold to mark differentially expressed TSS in MAplot (NA = Don't make an MAplot)

Value

A GRanges object containing p-values of differential expression for each TSS.

Examples

# before running this
# 1. Create a CapSet object
# 2. de-multiplex the fastqs
# 3. map them
# 4. filter duplicate reads from mapped BAM
# 5. detect TSS
# 6. fit the diff TSS model.

## Not run: 
# load a previously saved DGEGLM object from step 5
csfit <- load("diffTSS_fit.Rdata")
dir <- system.file("extdata", package = "icetea")
# detect differentially expressed TSS between groups (return MA plot)
detectDiffTSS(csfit, testGroup = "mut", controlGroup = "wt",
               tssFile = file.path(dir, "testTSS_merged.bed"), MAplot_fdr = 0.05)


## End(Not run)

## Not run: 
# load a previously saved DGEGLM object from step 5
csfit <- load("diffTSS_fit.Rdata")
dir <- system.file("extdata", package = "icetea")
# detect differentially expressed TSS between groups (return MA plot)
detectDiffTSS(csfit, testGroup = "mut", controlGroup = "wt", MAplot_fdr = 0.05)


## End(Not run)

vivekbhr/icetea documentation built on June 8, 2020, 4:45 a.m.