Illumina data

Description Usage Arguments Value Note See Also

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.

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

`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`.

a dataframe of counts.

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

pairwiseAlignSeqs, vpairwiseAlignSeqs, primerIDAlignSeqs, findLTRs, findPrimers, findAndTrimSeq