| getSubSeqsTable {mlgt} | R Documentation |
A list of sequences mapped to both thisMarker and thisSample is created and these sequences are aligned to markerSeq.
getSubSeqsTable(thisMarker, thisSample, sampleMap,
fMarkerMap, rMarkerMap, markerSeq, maxVarsToAlign = 30,
minTotalCount = 500, errorCorrect = FALSE,
correctThreshold = 0.01, minLength = 70)
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). |
This internal function is called by mlgt
A table of unique variants and their counts. The sequences have been trimmed to the portion aligned with markerSeq