plotGeneAlignDepth: plotGeneAlignDepth: Plots of read alignment depth for genetic...

Description Usage Arguments Details Author(s) Examples

Description

The function takes a bamReader and a refGenome object together with a gene name and an optional transcript name and plots the read alignment depth for the regtion of the gene in the opened BAM file. When transcript data is present, the exonic ranges are added as rectangles on a chromosomal line.

Usage

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plotGeneAlignDepth(reader, genome, 
            gene=NULL, transcript=NULL,
            log="y", cex.main=2,
            col="grey50", fill="grey90", grid=TRUE, 
            box.col="grey20", box.border="grey80")

Arguments

reader

bamReader (rbamtools). Must be opened and have initialized index.

genome

refGenome. Object which contains genomic annotatin data.

gene

character. Name of one single gene.

transcript

character (optional). Name of one single transcript.

log

character. Name of one single gene.

cex.main

numeric. Determines size of main title.

col

color. A color for align depth line.

fill

color. A color for the interior of align depth area.

grid

logical. When TRUE, a grid is drawn.

box.col

color. A color for the interior of exon rectangles.

box.border

color. A color for the border of exon rectangles.

Details

The function checks for opened bamReader and initialized index. When transcript name is given, the function will plot the positions of the transcript beneath the alignment depth.

Author(s)

Wolfgang Kaisers

Examples

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# Open bamReader
bam <- system.file("extdata","rna_fem.bam",package="spliceSites")
reader <- bamReader(bam, idx=TRUE)
# Load annotation data
ucf <- system.file("extdata", "uc_small.RData", package="spliceSites")
uc <- loadGenome(ucf)
plotGeneAlignDepth(reader, uc, gene="WASH7P", transcript="uc001aac.4")

spliceSites documentation built on May 6, 2019, 3:05 a.m.