alignReport: Report on alignment
In mlgt: Multi-Locus Geno-Typing

Description Usage Arguments Details Value See Also Examples

Inspect site frequency spectra for alignments.

  alignReport(mlgtResultObject,
    markers = names(mlgtResultObject@markers),
    samples = mlgtResultObject@samples,
    correctThreshold = 0.01,
    consThreshold = (1 - correctThreshold),
    profPlotWidth = 60, fileName = NULL, method = "table",
    warn = TRUE)

`mlgtResultObject`	an object of class `mlgtResult`
`markers`	Which markers to output
`samples`	Which samples to output
`correctThreshold`	A hypothetical level at which you migth correct low frequence variants. Default = 0.01.
`consThreshold`	(1- correctThreshold)
`profPlotWidth`	How many residues to plot in `profile` mode. Default=60.
`fileName`	Give a filename to export result to (pdf).
`method`	One of c("table", "profile", "hist"). "hist" plot a histogram of MAF frequencies. "profile" plots a coloured barplot represnting the allele frequencies at each site.
`warn`	Issue warnings (default = TRUE)

Produce different kinds of reports to assess quality of data for each marker/sample pair. Can be a good way to assess whether errorCorrect should be applied.

A data frame for each marker listing site statistics.

errorCorrect

## Not run: 
data("mlgtResult", package="mlgt")
alignReport(my.mlgt.Result,markers="DPA1_E2", samples="MID-22", method="profile")
alignReport(my.mlgt.Result,markers="DPA1_E2", samples="MID-22", method="hist")

## End(Not run)