findVector: Find vector DNA in reads and add results to SampleInfo...

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

Description

Given a sampleInfo object, the function finds vector fragments following the LTR piece 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' viral LTRs found in the sampleInfo object. The sequence itself is never trimmed but rather coordinates of vector portion is added to LTR coordinates and recorded back to the object and used subsequently by extractSeqs function to perform the trimming. This function heavily relies on blatSeqs. In order for this function to work, it needs vector sequence which is read in using 'vectorFile' metadata supplied in the sample information file in read.sampleInfo

Usage

findVector(sampleInfo, showStats = FALSE, parallel = TRUE,
  samplenames = NULL)

Arguments

sampleInfo	sample information SimpleList object outputted from findLTRs, which holds decoded, primed, and LTRed sequences for samples per sector/quadrant.
showStats	toggle output of search statistics. Default is FALSE.
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. Parllelization is done at sample level per sector. Use parallel2 for parallelization at sequence level.
samplenames	a vector of samplenames to process. Default is NULL, which processes all samples from sampleInfo object.

Value

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

Note

• If parallel=TRUE, then be sure to have a parallel backend registered before running the function. One can use any of the following MulticoreParam SnowParam

See Also

pairwiseAlignSeqs, blatSeqs, extractFeature, extractSeqs, findPrimers, findLTRs, findLinkers, findAndTrimSeq, findAndRemoveVector

Examples

load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
findVector(seqProps, showStats=TRUE)

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