getSonicAbund: Calculate breakpoint/sonic abundance of integration sites in...

In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given distinct fragment lengths per integration, the function calculates sonic abundance as described in sonicLength. This function is called by clusterSites and needs all individual fragments lengths per position to properly estimate the clonal abundance of an integration sites in a given population.

Usage

getSonicAbund(posID = NULL, fragLen = NULL, grouping = NULL,
  replicateNum = NULL, psl.rd = NULL, parallel = TRUE)

Arguments

posID	a vector of discrete positions, i.e. Chr,strand,Position. Required if psl.rd parameter is not defined.
fragLen	a vector of fragment length per posID. Required if psl.rd parameter is not defined.
grouping	additional vector of grouping of length posID or psl.rd by which to pool the rows (i.e. samplenames). Default is NULL.
replicateNum	an optional vector of the replicate number per grouping and posID. Default is NULL.
psl.rd	a GRanges object returned from getIntegrationSites Default is NULL.
parallel	use parallel backend to perform calculation with BiocParallel. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam. Process is split by the grouping the column.

Value

a data frame with estimated sonic abundance shown alongside with the original input. If psl.rd parameter is defined then a GRanges object is returned with a new column 'estAbund'.

Note

For samples isolated using traditional restriction digest method, the abundance will be inaccurate as it is designed for sonicated or sheared sample preparation method.

See Also

clusterSites, otuSites, findIntegrations, getIntegrationSites, pslToRangedObject

Examples

data("A1",package='sonicLength')
A1 <- droplevels(A1[1:1000,])
bore <- with(A1, getSonicAbund(locations, lengths, "A", replicates))
head(bore)

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.