View source: R/classes_methods.R
EstimateContaminationRate | R Documentation |
Based on mean read depth at blank and non-blank taxa, estimate sample
cross-contamination and add that information to the "RADdata"
object.
EstimateContaminationRate(object, ...) ## S3 method for class 'RADdata' EstimateContaminationRate(object, multiplier = 1, ...)
object |
A |
multiplier |
A single numeric value, or a named numeric vector with one value per blank
taxon in |
... |
Additional arguments (none implemented). |
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.
A "RADdata"
object identical to object
but with the
"contamRate"
attribute adjusted.
Lindsay V. Clark
# 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)
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