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

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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

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

# 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")

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.