annotateSites: Find the 5' primers and add results to SampleInfo object.

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

Description

Given a sampleInfo object, the function finds 5' primers for each sample per sector and adds the results back to the object. This is a specialized function which depends on many other functions shown in 'see also section' to perform specialized trimming of 5' primer/adaptor found in the sampleInfo object. The sequence itself is never trimmed but rather coordinates of primer portion is recorded back to the object and used subsequently by extractSeqs function to perform the trimming.

Usage

annotateSites(sampleInfo, annots = NULL, samplenames = NULL,
  parallel = TRUE, ...)

Arguments

sampleInfo	sample information SimpleList object outputted from findIntegrations, which holds genomic integration sites.
annots	a named list of GRanges object holding features for annotating integration sites. The name attribute of the list is used as column name.
samplenames	a vector of samplenames to process. Default is NULL, which processes all samples from sampleInfo object.
parallel	use parallel backend to perform calculation. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam. Parllelization is done at sample level per sector. Use parallel2 for parallelization at sequence level.
...	additional parameters to be passed to doAnnotation except for sites.rd, features.rd, and colnam.

Value

a SimpleList object similar to sampleInfo paramter supplied with new data added under each sector and sample. New data attributes include: primed

See Also

clusterSites, isuSites, crossOverCheck, findIntegrations, getIntegrationSites, pslToRangedObject

Examples

 

load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
data(genes)
genes <- makeGRanges(genes)
cpgs <- getUCSCtable("cpgIslandExt","CpG Islands")
cpgs <- makeGRanges(cbind(cpgs,strand="*"), chromCol = "chrom")
annots <- list("RefGenes"=genes,"CpG"=cpgs)
annotateSites(seqProps, annots, annotType="nearest", side="5p")

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