R: Align and trim sequences for marker/sample pair

getSubSeqsTable {mlgt} | R Documentation

## Align and trim sequences for marker/sample pair

### Description

A list of sequences mapped to both thisMarker and thisSample is created and these sequences are aligned to markerSeq.

### 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).

### Details

This internal function is called by `mlgt`

### Value

A table of unique variants and their counts. The sequences have been trimmed to the portion aligned with markerSeq

[Package mlgt version 0.16 Index]