checkRemoveIDs checks that the file names with the individuals to be filtered can be found. It reads the corresponding files, combines the selected individuals into one data.frame and compares these to all individuals in the analysis.
checkRemoveIDs(prefix, remove_individuals = NULL, keep_individuals)[character] Prefix of PLINK files, i.e. path/2/name.bed, path/2/name.bim and path/2/name.fam.
[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.
[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.
data.frame containing family (FID) and individual (IID) IDs of individuals to be removed from analysis.