strvalidator (version 1.0.0)

calculateBalance: Calculate balance

Description

calculateBalance calculates the inter and intra locus balance.

Usage

calculateBalance(data, ref, perSample = TRUE, lb = "prop", perDye = TRUE,
  hb = 1, ignoreCase = TRUE, debug = FALSE)

Arguments

data

a data frame containing at least 'Sample.Name', 'Marker', 'Height', 'Allele', and Dye'.

perSample

logical, default TRUE calculates balance for each sample, FALSE calculates the average across all samples.

lb

string. 'prop' is defualt and locus balance is calculated proportionally 'norm' locus balance is normalised in relation to the locus with the highest total peakheight.

perDye

logical, default is TRUE and locus balance is calculated within each dye. FALSE locus balance is calculated globally across all dyes.

hb

numerical, definition of heterozygous balance. hb=1; HMW/LMW, hb=2; Max1(Ph)/Max2(Ph).

ignoreCase

logical indicating if sample matching should ignore case.

Value

• data.frame with with columns 'Sample.Name', 'Marker', 'Delta', 'Hb', 'Lb', 'MPH'. Or 'Sample.Name', 'Marker', 'Delta.Mean', 'Hb.n', 'Hb.Min', 'Hb.Mean', 'Hb.Sd', 'Hb.95', 'Lb.n', 'Lb.Min', 'Lb.Mean', 'Lb.Sd'.

Details

Calculates the inter and intra locus balance for a dataset. Only peaks corresponding to reference alleles will be included in analysis (does not require filtered data). Also calculates the allele size difference between heterozygous alleles. Takes 'slimmed' data for samples and references as input. NB! Requires at least one row for each marker per sample, even if no data. NB! 'X' and 'Y' will be handled as '1' and '2' respectively.

Examples

data(ref2)
data(set2)
# Calculate average balances.
calculateBalance(data=set2, ref=ref2, perSample=FALSE)