polyRAD (version 1.1)

EstimateContaminationRate: Estimate Sample Contamination Using Blanks

Description

Based on mean read depth at blank and non-blank taxa, estimate sample cross-contamination and add that information to the "RADdata" object.

Usage

EstimateContaminationRate(object, ...)
# S3 method for RADdata
EstimateContaminationRate(object, multiplier = 1, …)

Arguments

object

A "RADdata" object where SetBlankTaxa has already been used to assign one or more taxa as blanks.

multiplier

A single numeric value, or a named numeric vector with one value per blank taxon in object, with names matching the blank taxa names. Read depth at blank taxa will be multiplied by this number when estimating sample cross-contamination. See example below.

…

Additional arguments (none implemented).

Value

A "RADdata" object identical to object but with the "contamRate" attribute adjusted.

Details

This function estimates sample cross-contamination assuming that the only source of contamination is from adapter or sample spill-over between wells during library preparation, or contamination among the libraries themselves. If you anticipate a higher rate of contamination during DNA extraction before library preparation, you may wish to increase the value using SetContamRate.

It is important to set the contamination rate to a reasonably accurate value (i.e. the right order of magnitude) in order for polyRAD to be able to identify homozygotes that may otherwise appear heterozygous due to contamination.

Examples

# NOT RUN {
# dataset for this example
data(Msi01genes)

# give the name of the taxon that is blank
Msi01genes <- SetBlankTaxa(Msi01genes, "blank")

# Fifteen libraries were done; blank is pooled over all of them, and
# most other samples are pooled over two libraries.
mymult <- 2/15

# estimate the contamination rate
Msi01genes <- EstimateContaminationRate(Msi01genes, multiplier = mymult)
# }