cdfg_port_samples: Chinook genotype data from 1974 individuals sampled by CA...

Description Usage Format References

Description

Chinook genotype data from 1974 individuals sampled by CA Dept of Fish and Game at California Ports

Usage

1

Format

This is a data frame with 1974 rows and 190 columns. Each row contains the genotype of a Chinook salmon that was caught in the ocean and sampled at a port. It was used for some analyses in Clemento et al. The row name is the name given to the fish. The 190 columns are the alleles carried at each of the 95 loci. This is in two-column format, so every locus gets two adjacent columns. The column headers have the names of the loci. The first occurrence of each locus is just the locus name and the second has a ".1" appended to it.

In general, alleles are coded as follows: A=1, C=2, G=3, T=4. There are some loci that get an allele code of 5, which refers to some data feature of some sort. You can think of it as an allele. There are only two alleles observed at each locus. Missing data are denoted by NAs.

References

Clemento AJ, Crandall ED, Garza JC, Anderson EC (2014) Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem. Fishery Bulletin 112(2-3): 112-130. doi:10.7755/FB.112.2-3.2


eriqande/SNPcontam documentation built on May 13, 2017, 8:20 p.m.