CheckLocusNames: Check for locus names that are not consistent between the two...

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

Description

Check for locus names that are not consistent between the two alleles of the same locus

Usage

CheckLocusNames(D)

Arguments

D

A data frame in which the loci start in column 1 and the column for the second allele at a locus named "LocusX" is "LocusX.1". Thus, it is the sort of data frame that would result from reading in a two-column (ToolKit) format file while setting the first column to be the row names, and using R's default method for making column names unique

Details

Note that if someone already added ".1" to the second occurrence of each locus name, then that will work fine as R will already find it to be unique (however adding ".a" or ".b" would break things).

Value

A matrix of the two instances of each locus name that are not identical in the file.

Examples

silly.data <- data.frame(LocA=c(2,2), LocA=c(3,2), LocB=c(45,42), LocBB=c(48,42))
  rownames(silly.data) <- c("Fish1", "Fish2")
  silly.data  # just look at it. Notice that LocB and LocBB aren't right!
  CheckLocusNames(silly.data)

  # note that the example steelhead data are OK
  CheckLocusNames(sthd.geno.A)

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