swfsc_chinook_baseline: Chinook genotype data from 8031 individuals across much of...

Description Usage Format References

Description

Chinook genotype data from 8031 individuals across much of the West Coast.

Usage

1

Format

This is a data frame with 8031 rows and 194 columns. Each row contains the genotype of a Chinook salmon included in the Southwest Fisheries Science Center's Chinook baseline. See Clemento et al. The first four columns are descriptive of each fish:

RepPop

A catenation of the individual's reporting unit and population of origin.

RepUnit

The reporting unit of population from which the fish came.

Pop

The population from which the individual fish came.

ID

A unique identifier for every individual. It turns out to be the RepPop catenated to a number.

The remaining 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. This data set is described in detail in Clemento et al 2014 and is also available on Dryad (see references)

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

Clemento AJ, Crandall ED, Garza JC, Anderson EC (2014) Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem. Dryad Digital Repository. doi:10.5061/dryad.574sv


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