plotCutDistribution {REDseq} | R Documentation |
plot cut frequencies of RE sites along a chromosome, which gives a bird-eye view of genome-wide frequent-cut regions and RE inaccessible regions.
plotCutDistribution(assignedSeqs,REmap, chr="chr1",xlim, title="RE cut frequency distribution", xlab="Chromosome Location (bp)",ylab="Frequency", round=TRUE, n.sequence)
assignedSeqs |
result returned from assignSeq2REsite |
REmap |
REmap used in assignSeq2REsite and generated from buildREmap |
chr |
chromosome to be plotted |
xlim |
range of x to be plotted |
title |
an overall title for the plot |
xlab |
a title for the x axis |
ylab |
a title for the y axis |
round |
TRUE: the sum of the weight is rounded up if the fraction part is greater than 0.5. FALSE: as it is. |
n.sequence |
total uniquely mapped sequences in the dataset for estimating the expected count for each RE site. If omitted, the expected count for each RE site will be set as 1 as default. |
Lihua Julie Zhu
assignSeq2REsite, distanceHistSeq2RE
library(REDseq) data(example.assignedREDseq) data(example.map) plotCutDistribution(example.assignedREDseq,example.map, chr="2", xlim =c(3012000, 3020000))