R: Report on alignment

alignReport {mlgt} | R Documentation

## Report on alignment

### Description

Inspect site frequency spectra for alignments.

### Usage

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

### Arguments

`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)

### Details

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.

### Value

A data frame for each marker listing site statistics.

### See Also

`errorCorrect`

### Examples

    ## 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)

[Package mlgt version 0.16 Index]