alignReport: 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)

Value

A data frame for each marker listing site statistics.

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.

Examples

Run this code

## 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)