position.barplot: Plot a barplot of alignments across a genome

In mw55309/viRome_legacy: Analysis and visualisation of short-read sequencing data from virus-infection studies

Description

For a given reference, plot the counts of alignments of reads of a given size-range along the positive and negative strands

Usage

position.barplot(vdf = NULL, minlen = 1, maxlen = 37, reflen = 10000, samp = "", plot=TRUE, poscol="red", negcol-"green")

Arguments

vdf	A data.frame as output from read.bam and clip.bam
minlen	The shortest read/alignment to include. The beginning of the range of read sizes you wish to count.
maxlen	The longest read/alignment to include. The maxlen of the range of read sizes you wish to count.
reflen	The length of the reference. You should probably know this, if you performed the alignment; otherwise it will be in the header of the SAM/BAM file
samp	The sample name associated with the data - to be used in the title of the resulting graph
plot	Whether or not to create a plot using default settings. Set to FALSE to suppress the plot. The data to allow you to draw your own graph will be returned anyway.
poscol	The colour of the positive bars. Default: "red"
negcol	The colour of the negative bars. Default: "green"

Details

This function calculates counts of the occurrence of reads/alignments of a given size-range across a genome. The x-axis is the genome position, the y-axis is the count, and bars point upwards for the positive strand, and downwards for the negative strand.

Plots a barplot to the current device and also returns a data.frame of the results. Plotting can be turned off with "plot=FALSE"

The value used for the position is the most 5' minlen of the alignment relative to the positive strand of the reference.

Value

Plots a barplot to the current device and also returns a data.frame of the results

position	The position in the reference
poscount	Count on the positive strand
negcount	Count on the negative strand

Author(s)

Mick Watson

See Also

barplot.bam, clip.bam

Examples

## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
## Not run: bam <- read.bam(bamfile=infile, chr="SINV", minlen=1, maxlen=11703, removeN=TRUE)
## Not run: bamc <- clip.bam(bam)

## Not run: bi <- position.barplot(vdf=bamc, minlen=21, maxlen=22, reflen=11703, samp="SRR389184")
## Not run: bi

mw55309/viRome_legacy documentation built on Dec. 21, 2021, 11:05 p.m.