SimCoImport {simco} | R Documentation |
This program imports Structure output files and turns them into a useable dataframe for use in R. Particularly for use by the "SimCoef()"
function of this package
SimCoImport(FILES)
FILES |
This is a list of the Structure files to be imported. |
The list of files is easily generated by putting the files in a directory, using "setwd()"
to change the working directory to that directory and then "list.files()"
to get the list.
The best way to use this command is by first setting your working directory to one containing the sample files using "setwd()"
.
Examples of structure output files, and further help, are provided in the docs
directory of the simco
package (which should be in your R library folder if you have installed simco
correctly.
For example:
setwd("/Users/orj/Documents/Simco/structurefiles")
myfiles<-list.files()
x<-SimCoImport(myfiles)
x
The output is a dataframe with columns of the confidence of assignment to a group and a run identifier (a CAPITAL letter). Rows are individual observations/samples.
Owen Jones
Rebbeck, CA, Jones, OR, & Tsai, IJ (unpublished) SimCo: A program to automate the comparison of multiple structure runs (available from owen.jones@imperial.ac.uk)
Pritchard, J. K. et al. (2000) Inference of population structure using multilocus genotype data. Genetics. 155, 945-959.