plotTSSprecision {icetea} | R Documentation

## Compare the precision of TSS detection between multiple samples

### Description

Plot precision of TSS detection from multiple samples (bed files) with respect to a given reference annotation.

Plot precision of TSS detection from multiple samples present within a `CapSet` object, with respect to a given reference annotation.

### Usage

    plotTSSprecision(
      reference,
      detectedTSS,
      distanceCutoff = 500,
      outFile = NULL,
      ...
    )

    ## S4 method for signature 'GRanges,character'
    plotTSSprecision(
      reference,
      detectedTSS,
      distanceCutoff = 500,
      outFile = NULL,
      sampleNames
    )

    ## S4 method for signature 'GRanges,CapSet'
    plotTSSprecision(
      reference,
      detectedTSS,
      distanceCutoff = 500,
      outFile = NULL,
      ...
    )

### Arguments

`reference` | Reference Transcrips/Genes as a `GRanges` object
`detectedTSS` | Either a CapSet object with TSS information (after running `detectTSS`) or a character vector with paths to the BED files containing detcted TSSs
`distanceCutoff` | integer. Maximum distance (in base pairs) from reference TSS to plot
`outFile` | character. Output file name (filename extention would be used to determine type) If outfile not specified, the plot would be returned on the screen
`...` | Additional arguments
`sampleNames` | character. Labels for input samples (in the same order as the input bed files)

### Value

A ggplot object, or a file. Plot showing perent of TSS detected per sample with respect to their cumulative distance to TSS of the provided reference

### Examples

    # load a txdb object
    suppressMessages(library("TxDb.Dmelanogaster.UCSC.dm6.ensGene"))
    seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"
    transcripts <- transcripts(TxDb.Dmelanogaster.UCSC.dm6.ensGene)

    # Plotting the precision using a pre computed set of TSS (.bed files) :

    tssfile <- system.file("extdata", "testTSS_merged.bed", package = "icetea")
    plotTSSprecision(reference = transcripts, detectedTSS = tssfile,
                    sampleNames = "testTSS", distanceCutoff = 500,
                    outFile = "TSS_detection_precision.png")

    ## Plotting the precision using a CapSet object :

    library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
    seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"
    # only use chrX to make the analysis faster
    seqlevels(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "X"
    transcripts <- transcripts(TxDb.Dmelanogaster.UCSC.dm6.ensGene)

    # load a previously saved CapSet object
    cs <- exampleCSobject()
    # plot
    plotTSSprecision(reference = transcripts, detectedTSS = cs,
                      outFile = "TSS_detection_precision.png")

[Package icetea version 1.8.0 Index]