README.md

In sq77/PCA7:

Consequences of SNP codings, PCA variants, and PCA graphs for elucidating population structure

This program was written by Cornell University undergraduate students Sheng Qian, Linda Zhou, and Rui Chen, supervised by Hugh G. Gauch Jr. This software is open source and may be redistributed or modified under the BSD 3-Clause License published by the Regents of the University of California.

This R code has been written for the purpose of in-house research, and it has been made public for the sake of transparency. Some researchers may find this program useful, but we neither guarantee its accuracy nor provide support to users.

DATA FILE FORMAT:

The first line has the number of columns (fastest changing subscript), a name for the columns, the number of rows, a name for the rows, and a name for the dataset; ideally, these names are 4 characters long. Data should be saved as a text file, so the example shown below could be given the filename GRAD.txt. The data are numeric, with values separated by one or more spaces (or a line break).

24 COLS 20 ROWS GRAD
1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1

INSTRUCTIONS:

To download and install the PCA7 package in R:

library(devtools)
install_github('ShengQian-Cornell/PCA7')

Each time you use this program, first set the working directory, ordinarily to the directory that contains the datafile to be analyzed, load the PCA7 package in R and type "PCA7()" in the console below in order to run this software.

setwd('working directory path')
library(PCA7)
PCA7()

sq77/PCA7 documentation built on May 15, 2019, 4:49 p.m.