mlgt-methods: Get variants for all markers/samples
In mlgt: Multi-Locus Geno-Typing

Description Usage Arguments Details Value See Also

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.

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

`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).

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.

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

prepareMlgtRun

mlgt documentation built on May 1, 2019, 8:45 p.m.