strvalidator (version 0.3.0)

calculateDropout: Calculate drop-out events

Description

calculateDropout calculate drop-out events (allele and locus) and records the surviving peak height.

Usage

calculateDropout(data, ref, ignoreCase = TRUE,
    debug = FALSE)

Arguments

data

data frame in GeneMapper format containing at least a column 'Allele'.

ref

data frame in GeneMapper format.

ignoreCase

logical, default TRUE for case insensitive.

debug

logical indicating printing debug information.

Value

• data.frame with columns 'Sample.Name', 'Marker', 'Allele', 'Height', 'Dropout', 'Rfu', and 'Heterozygous'. Dropout: 0 indicate no dropout, 1 indicate allele dropout, and 2 indicate locus dropout. Rfu: height of surviving allele. Heterozygous: 1 for heterozygous and 0 for homozygous.

Details

Calculates drop-out events. In case of allele dropout the peak height of the surviving allele is given. Homozygous alleles in the reference set can be either single or double notation (X or X X). Markers present in the reference set but not in the data set will be added to the result. NB! "Sample Names" in 'ref' must be unique 'core' name of replicate sample names in 'data'. Use checkSubset to make sure subsetting works as intended.

Examples

data(set4)
data(ref4)
drop <- calculateDropout(data=set4, ref=ref4, ignoreCase=TRUE)