R: Get variants for all markers/samples

mlgt {mlgt} | R Documentation

## Get variants for all markers/samples

### Description

`mlgt` Works through all pairs of markers and samples. Aligns variants and trims aligned variants to the marker sequence. Potential 'alleles' are assigned from the most common variants within each sample.

### Usage

      mlgt(designObject, maxVarsToAlign = 30,
        minTotalCount = 500, errorCorrect = FALSE,
        correctThreshold = 0.01, minLength = 70)

### Arguments

`designObject` | an object of class `mlgtDesign`
`minTotalCount` | How many assigned sequences to allow before limiting the number of raw variants to allign.
`maxVarsToAlign` | If total assigned sequences exceeds 'minTotalCount', then only the 'maxVarsToAlign' most abundant variants are used.
`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

Depends upon `prepareMlgtRun` having been run in the current directory to generate designObject of class `mlgtDesign`. The basic process for each marker/sample pair is to align all unique variants using MUSCLE and then extract the alignment portion aligned to the reference marker sequence, ignoring the rest. The marker alignment is critical and `mlgt` has several options to optimise this alignment. If the total number of reads is less than minTotalCount, then all variants are aligned. Otherwise, only the most abundant 30 unique variants are aligned. Optionally, alignments are ‘error-correted’ as per the separate function `errorCorrect`. Reads shorter than 'minLength' are filtered out.

### Value

an object of class `mlgtResult` containing all variants and their counts, a summary table (all markers) and one summary table per marker.

### See Also

`prepareMlgtRun`

[Package mlgt version 0.16 Index]