troubleshootLinkers: Compare LTRed/Primed sequences to all linkers.

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

Description

Given a SampleInfo object, the function compares LTRed sequences from each sample per sector to all the linker sequences present in the run. The output is a summary table of counts of good matches to all the linkers per sample.

Usage

troubleshootLinkers(
  sampleInfo,
  qualityThreshold = 0.55,
  qualityThreshold1 = 0.75,
  qualityThreshold2 = 0.5,
  doRC = TRUE,
  parallel = TRUE,
  samplenames = NULL,
  ...
)

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.
qualityThreshold	percent of linker length to match, round(nchar(linker)*qualityThreshold). Default is 0.55. Only applies to non-primerID based linkers
qualityThreshold1	percent of first part of patternSeq to match. Default is 0.75. Only applies to primerID based linker search.
qualityThreshold2	percent of second part of patternSeq to match. Default is 0.50. Only applies to primerID based linker search.
doRC	perform reverse complement search of the linker sequence. Default is TRUE. Highly recommended!
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.
...	extra parameters to be passed to pairwiseAlignment.

Value

a dataframe of counts.

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, vpairwiseAlignSeqs, primerIDAlignSeqs, findLTRs, findPrimers, findAndTrimSeq

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