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 1.31.0 Index]