swfsc.mega.tools: Streamlining SWFSC Molecular Genetics and Analysis Team...

In eriqande/swfsc.mega.tools: Tools for manipulating and analyzing genetic data at the Santa Cruz Lab

Description

swfsc.mega.tools is a nascent effort to bring together bits of R code that we have written for various applications into a single R package that everyone in the lab should find easy to use.

Details

Utlimately we hope that it will include functions that will assist in a variety of analyses we do in the lab. The several areas that the package addresses are detailed below.

Standardizing Files of Genotypes

Our lab has a frightening mound of genetic data sets that were collected over various time periods and by various people in the lab. Some of these data may remain in that state, but in the effort to extract data from these files for loci that will continue to use going forward we've got some tools here.

• Locus Sets:The package includes names for loci that have been stanardized and should be used moving forward. These are stored as simple character vectors. Currently you will find: Omykiss.Standard.Loci

• Functions:The function CompareLocusNames lets you compare the locus headers in a file (read into a data frame) with another file or with a string of locus names, like Omykiss.Standard.Loci. Some small functions related to this that might be found to be helpful are: ExcelColumns, and FindLocusColumns.

Datasets

Currently we don't have any standardized data sets in this package, but we may include some (like our baseline files, etc). Until that time however, the package includes some small data sets, like sthd.geno.A and sthd.geno.B for use in function examples.

eriqande/swfsc.mega.tools documentation built on May 16, 2019, 8:48 a.m.