Description Usage Format Source References Examples
The dataset uses a subset of makers from 6K SNP genotyping array to compute paternity index.
1 |
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)
Simulated dataset
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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))
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