CompareLocusNames: find closely matching locus names between two files

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

Description

find closely matching locus names between two files

Usage

CompareLocusNames(First, Second, maxD = 7)

Arguments

First	Either a vector of locus names, or 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
Second	a vector of locus names or a data frame formatted like First.
maxD	The maximum string distance between two locus names that are still considered an approximate match

Value

A list with three components:

• InFirstButNotSecond: Loci appearing in First but with no exact matches in Second

• RemainingInSecondButNotInFirst: Any loci in second that had neither approximate nor exact matches to any loci in First.

• InBoth: Loci that have an exact matching name in both First and Second.

Each component of the returned list has a matrix with 5 columns with headers as follows:

• NameInFirst: Locus name as it appears in First

• NameInSecond: Locus name as it appears in Second

• StringSimilarity: The distance between the two approximately matching names. Lower means more similar.

• ColumnsInFirst: If First is a data.frame, these correspond to the columns in an excel file that hold the original data table.

• ColumnsInSecond: See above, but for second.

Examples

# look for closely matching locus names between the two steelhead example data sets
 CompareLocusNames(sthd.geno.A, sthd.geno.B)

 # look for the standard Omykiss locus names in sthd.geno.B
 CompareLocusNames(sthd.geno.B, Omykiss.Standard.Loci)

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