paternityIndex: Calculation of composite paternity index using SNP data

In paternity: Paternity tests using SNPs

Description

The function computes composite paternity index based on SNP data useful for confirming paternity. The paternity index are calculation based on no mutations or no technical error. High quality data, preferably confirmed genotypes with multiple assays are desirable. The package is for research purpose only not for legal or diagnostic purpose.

Usage

paternityIndex(dataframe, marker = "marker", mother = "mother", child = "child",
      AF = "AF", Afreq = "a", Bfreq = "b", afcalcol = NA)

Arguments

dataframe	name of dataframe used in the analysis, should have information on marker name, SNP data in AB format, Allele frequencies (A and B columns)
marker	name of marker column
mother	Name of mother or known parent column used in analysis
child	Name of child column used in analysis
AF	Alleged parent (father or mother) used in analysis
Afreq	Frequency A alleles (0 to 1), "calculate" with use the specified data range in afcalcol to calculate alelele frequency. Note that the individuals are in columns the markers are in rows.
Bfreq	Frequency of B alleles (0 t0 1), "calculate" with use the specified data range in afcalcol to calculate alelele frequency. Note that the individuals are in columns the markers are in rows.
afcalcol	column range (start:end), where the data for calculating allele frequency is stored Afreq or Bfreq should be "calculate", in case where the allele frequency are estimated from the data itself.

Value

Returns log (composite paternity index) between the Alleged parent (father) and child

Author(s)

Umesh Rosyara

References

Elston, R.C. 1986. Probability and paternity testing. Am.. J.. Human Genetics 39: 112-122

Evett, I.W., and B.S. Weir.1998. Interpreting DNA evidence. Sunderland, MA: Sinauer Associates, Inc.

Examples

data(patdatSNP)
 pind <- paternityIndex (dataframe =patdatSNP , marker = "SNPmarker", 
 mother = "Mother", child = "Child", AF = "AFather1", Afreq = "a",
  Bfreq = "b", afcalcol = NA)
 # log composite paternity index 
 log(prod(pind$PI))
 
 # allele calculated from the dataset provided in columns afcalcol
pind1 <- paternityIndex (dataframe =patdatSNP , marker = "SNPmarker", 
mother = "Mother",  child = "Child", AF = "AFather1", Afreq = "calculate",
 Bfreq = "calculate", afcalcol = 4:15)
  log(prod(pind1$PI)) 
 

paternity documentation built on May 2, 2019, 5:25 p.m.