Cherry paternity analysis dataset

Description

The dataset uses a subset of makers from 6K SNP genotyping array to compute paternity index.

Usage

1

Format

A data frame with 39 observations on the following 20 variables.

SNPmarker

Name of SNP markers

Chr

Chromsome where SNP is located

a

A alelle frequency

b

B allele frequency

Child

SNP marker scores for individual named Child (AA, AB, BB)

Mother

SNP marker scores (AA, AB, BB)

AFather1

SNP marker scores (AA, AB, BB)

AFather2

SNP marker scores (AA, AB, BB)

AFather3

SNP marker scores (AA, AB, BB)

AFather4

SNP marker scores (AA, AB, BB)

AFather5

SNP marker scores (AA, AB, BB)

AFather6

SNP marker scores (AA, AB, BB)

AFather7

SNP marker scores (AA, AB, BB)

AFather8

SNP marker scores (AA, AB, BB)

AFather9

SNP marker scores (AA, AB, BB)

Source

Simulated dataset

References

Rosyara UR, Sebolt AM, Peace C and Iezzoni AF.Identification of the paternal parent for the sweet cherry (Prunus avium L.) cultivar 'Bing' and confirmation of descendants using SNP markers

Examples

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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))
 
 # second case for AFather2 
  pind1 <- paternityIndex (dataframe =patdatSNP , marker = "SNPmarker", 
 mother = "Mother",  child = "Child", AF = "AFather2", Afreq = "a", 
 Bfreq = "b", afcalcol = NA)
 # log composite paternity index 
 log(prod(pind1$PI))
 
 # allele calculated from the dataset provided in columns afcalcol
pind2 <- paternityIndex (dataframe =patdatSNP , marker = "SNPmarker", 
mother = "Mother", child = "Child", AF = "AFather1", Afreq = "calculate",
 Bfreq = "calculate", afcalcol = 4:15)
  log(prod(pind2$PI))