Table 1 Input formats supported by the function ipcaps
From: IPCAPS: an R package for iterative pruning to capture population structure
Input formats | Descriptions |
|---|---|
PLINK binary format | PLINK binary format consist of 3 files; bed, bim, and fam. To generate these files from PLINK, use option --make-bed |
Text format | The functions ipcaps supports SNPs in additive coding (0 = AA, 1 = AB, 2 = BB). Each row represents SNP, and each column represents individual. SNPs need to be separated by a space or a Tab. A big text file should be divided into smaller files to load faster. To input several files, set the option as, for example, files = c(‘input1.txt’,‘input2.txt’,‘input3.txt’) |
RData format | In the case of re-analysis, it is convenient to rerun the function ipcaps using the file rawdata. RData is generated by the function ipcaps itself. This file contains a vector of labels and a matrix of SNPs containing N rows of individuals and M columns of SNPs. |