Description Usage Arguments Value Author(s) References Examples
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.
1 2 | paternityIndex(dataframe, marker = "marker", mother = "mother", child = "child",
AF = "AF", Afreq = "a", Bfreq = "b", afcalcol = NA)
|
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. |
Returns log (composite paternity index) between the Alleged parent (father) and child
Umesh Rosyara
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.