troubleshootLinkers: Compare LTRed/Primed sequences to all linkers.

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.

Description

Usage

Arguments

Value

See Also