findPrimers: Find the 5' primers 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 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

findPrimers(
  sampleInfo,
  alignWay = "slow",
  showStats = FALSE,
  doRC = FALSE,
  parallel = TRUE,
  samplenames = NULL,
  bypassChecks = FALSE,
  parallel2 = FALSE,
  ...
)

Arguments

sampleInfo	sample information SimpleList object outputted from findBarcodes, which holds decoded sequences for samples per sector/quadrant along with information of sample to primer associations.
alignWay	method to utilize for detecting the primers. One of following: "slow" (Default), or "fast". Fast, calls vpairwiseAlignSeqs and uses vmatchPattern at its core, which is less accurate with indels and mismatches but much faster. Slow, calls pairwiseAlignSeqs and uses pairwiseAlignment at its core, which is accurate with indels and mismatches but slower.
showStats	toggle output of search statistics. Default is FALSE.
doRC	perform reverse complement search of the defined pattern/primer. Default is FALSE.
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.
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 either vmatchPattern or pairwiseAlignment depending on 'alignWay' parameter.

Value

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

Note

• For paired end data, qualityThreshold for pair 2 is decreased by 0.10 to increase chances of matching primer 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, findLTRs, findLinkers, findAndTrimSeq

Examples

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

## End(Not run)

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