plink2cape | R Documentation |
Convert plink2 files to cape format
plink2cape( ped = "test.ped", map = "test.map", pheno = "test.pheno", out = "out.csv", missing_genotype = "0", no_fid = FALSE, no_parents = FALSE, no_sex = FALSE, no_pheno = FALSE, verbose = FALSE, overwrite = FALSE )
ped |
full path to the ped file |
map |
full path to the map file |
pheno |
full path to the pheno file |
out |
full path to the output file |
missing_genotype |
default is "0" |
no_fid |
boolean, default is FALSE |
no_parents |
boolean, default is FALSE |
no_sex |
boolean, default is FALSE |
no_pheno |
boolean, default is FALSE |
verbose |
boolean, default is FALSE, gives some happy little progress messages |
overwrite |
boolean, default is FALSE, will only remove the existing file if this is set to TRUE |
For further information about PLINK and its file formats, see https://zzz.bwh.harvard.edu/plink/
A list with two elements: data_obj and geno_obj
These objects are formatted for use in cape and must then
be separated to use in run_cape
.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
## Not run: #convert files with default names to a data_obj data_obj <- plink2cape() ## End(Not run)
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