findLTRs: Find the 5' LTRs 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' LTR following the primer 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 LTR portion is added to primer coordinates and recorded back to the object and used subsequently by extractSeqs function to perform the trimming. This function heavily relies on pairwiseAlignSeqs.

Usage

findLTRs(sampleInfo, showStats = FALSE, doRC = FALSE,
  parallel = TRUE, samplenames = NULL, bypassChecks = FALSE,
  parallel2 = FALSE, ...)

Arguments

sampleInfo	sample information SimpleList object outputted from findPrimers, which holds decoded and primed sequences for samples per sector/quadrant along with information of sample to LTR associations.
showStats	toggle output of search statistics. Default is FALSE. For paired end data, stats for "pair2" is relative to decoded and/or primed reads.
doRC	perform reverse complement search of the defined pattern/LTR sequence. 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.
samplenames	a vector of samplenames to process. Default is NULL, which processes all samples from sampleInfo object.
bypassChecks	skip checkpoints which detect if something was odd with the data? Default is FALSE.
parallel2	perform parallelization is sequence level. Default is FALSE. Useful in cases where each sector has only one sample with numerous sequences.
...	extra parameters to be passed to pairwiseAlignment.

Value

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

Note

• For paired end data, qualityThreshold for pair 2 is decreased by 0.05 to increase chances of matching LTR sequence.

• 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, vpairwiseAlignSeqs, extractFeature, extractSeqs, primerIDAlignSeqs, findPrimers, findLinkers, findAndTrimSeq

Examples

 

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

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