insert.size.hist {TEQC} | R Documentation |
Computes read pair insert sizes, i.e. distance from first base of first read to last base of second read of a read pair, and plots a histogram for all insert sizes.
insert.size.hist(readpairs, returnInserts = FALSE, legendpos="topleft", outline=FALSE, main, xlab, ylab, breaks, col, ...)
readpairs |
|
returnInserts |
if |
legendpos |
position of the legend, e.g. 'topleft' or 'topright' |
outline |
if |
main |
plot title |
xlab, ylab |
x- and y-axis labels |
breaks |
e.g. integer specifying the number of cells for the histogram, see |
col |
histogram color |
... |
further graphical parameters passed to |
Histogram of read pair insert sizes. Average, standard deviation and median insert size are given in the legend and indicated by lines.
If returnInserts = TRUE
, a named vector of insert sizes is returned.
Manuela Hummel m.hummel@dkfz.de
get.reads
, reads2pairs
, duplicates.barplot
## get reads exptPath <- system.file("extdata", package="TEQC") readsfile <- file.path(exptPath, "ExampleSet_Reads.bed") reads <- get.reads(readsfile, idcol=4, skip=0) ## merge to read pairs readpairs <- reads2pairs(reads) ## insert size histogram insert.size.hist(readpairs, breaks=10)