read.dist.plot: Plot distances between 5' ends of reads on complementary...

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

Description

Plot a graph and produce a data.frame, ready for plotting, that counts the distances between the 5' end of reads on opposite strands

Usage

read.dist.plot(sr = NULL, minlen = 1, maxlen = 37, method = "add", pad = 30, primary = "pos", plot=TRUE, title="5' read distance plot", xlab="Distance", ylab="Count")

Arguments

sr	Sequence report as output by sequence.report
start	The minimum length of mapped read to consider
end	The maximum length of mapped read to consider
method	Must be one of c("pos", "neg", "mean", "multiply", "add", "min", "max"); mean (takes the mean of counts on opposite strands), pos (counts reads on the pos strand only), neg (counts reads on the neg strand only), multiply (multiplies count of pos with count of neg), add (adds counts of pos and neg), min (minimum of pos and neg counts) and max (maximum of pos and neg counts)
pad	Distance to pad either side of the 5' end to look for overlaps
primary	Whether the positive or negative strand is iterated over first. Acceptes "pos" or "neg"
plot	Whether or not to plot to the current device. Default TRUE
title	Title for the plot. Ignored is plot==FALSE
xlab	X axis labels for the plot. Ignored is plot==FALSE
ylab	Y axis labels for the plot. Ignored is plot==FALSE

Details

This function can be used to look for enrichment of particular distances between reads on opposite strands: for example, it has been shown in quite a few publications that the piRNA response (25-29bp) is characterised by reads on complementary strands whose 5' ends overlap by 10bp.

This function is more generic, and just summarises distances between the 5' ends of reads on opposite strands.

The main issue is which summary function one chooses. For example, let us say that we have 10 reads on the positive strand whose 5' end map at position 50; we also have 20 reads on the negative strand whose 5' ends map at position 59. The distance between the 5' ends is +10: but how many reads do we count as having that distance? Is it 10 (pos)? 20 (neg)? min(10,20)? max(10,20)? mean(10,20)? 10 * 20 (multiply)? You may decide, though we set the default as "add".

Value

Data frame with values:

loc	Distance between 5' ends
count	Cumulative function (see "method") of reads that are "loc" distance apart at the 5' end

Author(s)

Mick Watson

Examples

 ## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
 ## Not run: bam <- read.bam(bamfile=infile, chr="SINV", start=1, end=12000, removeN=TRUE)
 ## Not run: bamc <- clip.bam(bam)
 ## Not run: sr <- sequence.report(bamc)
 ## Not run: sr
 ## Not run: rd <- read.dist.plot(sr, minlen=25, maxlen=29)
 

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