readAnnotation {srnadiff} | R Documentation

## Reads and parses GFF/GTF files

### Description

`readAnnotation` reads and parses content of GFF/GTF files and stores annotated genomic features (regions) in a `GRanges` object.

### Usage

    readAnnotation(fileName, feature = NULL, source = NULL, tagName = NULL)

### Arguments

`fileName` | A path, URL or connection to the GFF/GTF annotation file. Compressed files (`"gz"`, `"bz2"` and `"xz"`) are handled transparently.
`feature` | `NULL` (the default) or a character vector of valid feature types. If not `NULL`, then only the features of the specified type(s) are imported.
`source` | `NULL` (the default) or a character vector of valid source types. If not `NULL`, then only the sources of the specified type(s) are imported.
`tagName` | `NULL` (the default). If not `NULL`, use this tag as systematic name for the elements of the `GRanges` object.

### Details

`feature` and `source` can be `NULL`. In this case, no selection is performed and all content into the file is imported. If `tagName` is `NULL`, then a systematic name (`annot.N`) is given to elements of the `GRanges` object.

### Value

A `GRanges` object with annotated regions information.

### See Also

`GFFFile-class`

### Examples

    ##-----------------------------------------------------------------------
    ## Extraction of miRNAs using an GTF annotation file
    ##-----------------------------------------------------------------------
    basedir  <- system.file("extdata", package="srnadiff", mustWork = TRUE)
    gtfFile  <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz")
    annotReg <- readAnnotation(gtfFile, feature="gene", source="miRNA")
    annotReg

    ##-----------------------------------------------------------------------
    ## Extraction of mature miRNAs using a miRBase-formatted file
    ##-----------------------------------------------------------------------
    basedir  <- system.file("extdata", package="srnadiff", mustWork = TRUE)
    gffFile  <- file.path(basedir, "mirbase21_GRCh38.gff3")
    annotReg <- readAnnotation(gffFile, feature="miRNA", tagName="miRNA")
    annotReg

    ##-----------------------------------------------------------------------
    ## Extraction of precursor miRNAs using a miRBase-formatted file
    ##-----------------------------------------------------------------------
    basedir  <- system.file("extdata", package="srnadiff", mustWork = TRUE)
    gffFile  <- file.path(basedir, "mirbase21_GRCh38.gff3")
    annotReg <- readAnnotation(gffFile, feature="miRNA_primary_transcript")
    annotReg

[Package srnadiff version 1.14.0 Index]