annotateTSS {icetea} | R Documentation

## Annotate the provided Transcription Start Sites

### Description

This function annotates the provided TSS bed file to provide the number of TSS falling within the genomic features from a given TxDB object. In order to break ties between overlapping features, the function ranks the features by preference. By default, the following order is used: fiveUTR > promoter > intron > coding > spliceSite > threeUTR > intergenic. A custom order of feature ranks can also be provided.

### Usage

    annotateTSS(
      tssBED,
      txdb,
      featureRank = c("fiveUTR", "promoter", "intron", "coding", "spliceSite", "threeUTR",
        "intergenic"),
      plotValue = "number",
      outFile = NULL
    )

### Arguments

`tssBED` | A bed file with detected TSS/differential TSS coordinates
`txdb` | A txdb object.
`featureRank` | A vector with features to use for breaking ties, in decending order of preference (highest to lowest),
`plotValue` | What values to plot (choose from "number", "percent" or NULL for no plot)
`outFile` | Output file name. (filename extention would be used to determine type). If outfile not specified, the plot would be retured on the screen

### Value

A data.frame with number of TSS falling into each feature

### Examples

    # load a txdb object
    library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
    seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"
    # limiting the annotation to X chromosome
    seqlevels(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "X"

    # annotate a given TSS bed file
    dir <- system.file("extdata", package = "icetea")
    tss <- file.path(dir, "testTSS_merged.bed")
    annotations <- annotateTSS(tssBED = tss, TxDb.Dmelanogaster.UCSC.dm6.ensGene,
                   plotValue = "number", outFile = "TSS_annot.pdf")

[Package icetea version 1.8.0 Index]