detectDiffTSS {icetea} | R Documentation

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

### 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)

[Package icetea version 1.8.0 Index]