plotInsertions: plotInsertions

In robinweide/tagmeppr: A computational pipeline to map tagmap-insertions

Description

Identify highly likely insertion-sites in an tagMeppr-object.

Usage

plotInsertions(exp, chrom = paste0("chr", c(1:25, "X")),
  colours = NULL, sideBySide = F, p = 0.05, showOrientation = F)

Arguments

exp	A list or singular instance of tagMeppr-object(s): first run findInsertions.
chrom	Which chromosomes should be plotted (even when no insertions are found).
colours	Choose colours for individual tagMeppr-objects (if sideBySide = T).
sideBySide	If true, will show per-object ideogram. If false, will show
p	Set a p-value treshold all (colour-coded) objects inside one ideogram.
showOrientation	Split hits on orientation.

Value

An object of the class ggplot.

Author(s)

Robin H. van der Weide, [e-mail]

Examples

## Not run: 
reference_hg19_PB = makeIndex(indexPath = '/home/A.Dent/analysis42/',
                              bsgenome = 'BSgenome.Hsapiens.UCSC.hg19',
                              ITR = 'PiggyBac')

C9 = newTagMeppr(F1 = 'clone9_FWD_R1.fq.gz',
                 F2 = 'clone9_FWD_R2.fq.gz',
                 R1 = 'clone9_REV_R1.fq.gz',
                 R2 = 'clone9_REV_R2.fq.gz',
                 name = "clone9",
                 protocol = 'PiggyBac')

align(exp = C9, ref = reference_hg19_PB, cores = 30, empericalCentre = T)

findInsertions(exp = C9, ref = reference_hg19_PB)

plotInsertions(exp = C9, chrom = c('chr1','chr2'))


## End(Not run)

robinweide/tagmeppr documentation built on Feb. 26, 2020, 10:41 p.m.