findLinkers: Find the 3' linkers and add results to SampleInfo object.

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

Description

Given a sampleInfo object, the function finds 3' linkers 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 3' primer/linker adaptor sequence found in the sampleInfo object. The sequence itself is never trimmed but rather coordinates of linker portion is recorded back to the object and used subsequently by extractSeqs function to perform the trimming. This function heavily relies on either pairwiseAlignSeqs or primerIDAlignSeqs depending upon whether linkers getting aligned have primerID in it or not.

Usage

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

Arguments

sampleInfo	sample information SimpleList object outputted from findPrimers or findLTRs, which holds decoded sequences for samples per sector/quadrant along with information of sample to primer associations.
showStats	toggle output of search statistics. Default is FALSE.
doRC	perform reverse complement search of the defined pattern/linker 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: linkered. If linkers have primerID then, primerIDs attribute is appended as well.

Note

• For paired end data, qualityThreshold for pair 2 is increased by 0.25 or set to 1 whichever is lower to increase quality & full match to linker sequence.

• If no linker matches are found with default options, then try doRC=TRUE.

• 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, primerIDAlignSeqs, findLTRs, findPrimers, extractFeature, extractSeqs, findAndTrimSeq, findIntegrations

Examples

 
## Not run: 
load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
findLinkers(seqProps, showStats=TRUE, doRC=TRUE)

## End(Not run)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.