findInsertions: findInsertions

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

Description

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

Usage

findInsertions(exp, ref, padding = NULL)

Arguments

exp	The tagMeppr-object of a sample: first run align.
ref	A reference object of makeIndex or loadIndex.
padding	Add padding to the start/end of reads in relation to the TIS. Default is half of the TIS (i.e. 2bp whit Piggybac), meaning that the mapper can report a match Xbp further than the TIS (i.e. TTAA).

Value

The object will be updated with a results-table:

fwdCount

Forward read-counts at this insertion-site

fwdOrient

Forward read-orientation at the insertion

D_FWD

The imbalance of forward reads on both sides of the site: D = 0 means no imbalance

fwdBinom

The probability of the imbalance

revCount

Reverse read-counts at this insertion-site

revOrient

Reverse read-orientation at the insertion

D_REV

The imbalance of forward reads on both sides of the site: D = 0 means no imbalance

revBinom

The probability of the imbalance

pMarkerMeppR

The combined probability of the imbalances

padj

Bonferroni-adjusted probabilties

orientation

The orientation of the insertion

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)

## End(Not run)

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