calculateHb: Calculate Heterozygote Balance

Description

Calculates the heterozygote (intra-locus) peak balance.

Usage

calculateHb(
  data,
  ref,
  hb = 1,
  kit = NULL,
  sex.rm = FALSE,
  qs.rm = FALSE,
  ignore.case = TRUE,
  exact = FALSE,
  word = FALSE,
  debug = FALSE
)

Value

data.frame with with columns 'Sample.Name', 'Marker', 'Delta', 'Hb', 'MPH'.

Arguments

data: a data frame containing at least 'Sample.Name', 'Marker', 'Height', and 'Allele'.
ref: a data frame containing at least 'Sample.Name', 'Marker', 'Allele'.
hb: numerical, definition of heterozygote balance. Default is hb=1. hb=1: HMW/LMW, hb=2: LMW/HMW, hb=3; min(Ph)/max(Ph).
kit: character defining the kit used. If NULL automatic detection is attempted.
sex.rm: logical TRUE removes sex markers defined by 'kit'.
qs.rm: logical TRUE removes quality sensors defined by 'kit'.
ignore.case: logical indicating if sample matching should ignore case.
exact: logical indicating if exact sample matching should be used.
word: logical indicating if word boundaries should be added before sample matching.
debug: logical indicating printing debug information.

Details

Calculates the heterozygote (intra-locus) peak balance for a dataset. Known allele peaks will be extracted using the reference prior to analysis. Calculates the heterozygote balance (Hb), size difference between heterozygous alleles (Delta), and mean peak height (MPH). NB! 'X' and 'Y' will be handled as '1' and '2' respectively.

Examples

Run this code

data(ref2)
data(set2)
# Calculate average balances.
calculateHb(data = set2, ref = ref2)