addGeneAligns {spliceSites} | R Documentation

## Reads a bamRange object for a given `bamReader`, `refGenome` and gene name.

### Description

Locates gene in genome via `refGenome` and reads a `bamRange` from the determined region.

### Usage

        addGeneAligns(x)

### Arguments

`x` | gapSites. The result contains a copy of the passed object.

### Details

The function adds a `gene_aligns` column to the contained `data.frame`.

### Value

gapSites

### Author(s)

Wolfgang Kaisers

### Examples

    # A) Read gapSites
    bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader <- bamReader(bam, idx=TRUE)
    ga <- alignGapList(reader)
    bamClose(reader)

    # B) Annotate
    ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
    ucj <- loadGenome(ucf)
    annotation(ga) <- annotate(ga, ucj)

    # C) align part
    gal <- addGeneAligns(ga)
    gal

[Package spliceSites version 1.30.0 Index]