plotSite: plotSite

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

Description

Plot the read distribution of an insertion.

Usage

plotSite(exp, site = 1, forceDetail = F, maxReads = Inf)

Arguments

exp	A list or singular instance of tagMeppr-object(s): first run findInsertions.
site	Which insertion should be plotted?
forceDetail	Even with more than 1000reds, still use the high-detail version.
maxReads	Set the maximum number of reads. If forward and/or reverse exceeds this, they will be downsampled to this number.

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)

plotSite(exp = C9, site = 1)


## End(Not run)

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