Usage
getSubSeqsTable(thisMarker, thisSample, sampleMap, fMarkerMap, rMarkerMap, markerSeq, maxVarsToAlign = 30, minTotalCount = 500, errorCorrect = FALSE, correctThreshold = 0.01, minLength = 70)
Arguments
thisMarker
A specific marker name
thisSample
A specific sample name
sampleMap
A list of sequence IDs assigned to each
marker. Each element named by marker name.
fMarkerMap
A list of sequence IDs assigned to each
sample using BLAST hits in forward orientation. Each
element named by sample name.
rMarkerMap
A list of sequence IDs assigned to each
sample using BLAST hits in reverse orientation. Each
element named by sample name.
markerSeq
The sequence of thisMarker
maxVarsToAlign
If total assigned sequences exceeds
'minTotalCount', then only the 'maxVarsToAlign' most
abundant variants are used.
minTotalCount
How many assigned sequences to allow
before limiting the number of raw variants to allign.
errorCorrect
Use error correection on alignment of
raw variants
correctThreshold
Maximum proportion of raw reads
at which (minor allele) bases and gaps are corrected.
minLength
Reads below this length are excluded
(they are very likely to be primer-dimers).