Read Plink FAM and covariates files
Read Plink FAM and covariates files.
Read_Plink_FAM(Filename, Is.binary=TRUE, flag1=0) Read_Plink_FAM_Cov(Filename, File_Cov, Is.binary=TRUE, flag1=0, cov_header=TRUE)
Filename |
input file name of plink FAM file |
Is.binary |
if TRUE, the phenotype is binary. If phenotype is continuous, it should be FALSE |
flag1 |
0 represents the default coding of unaffected/affected (1/2) (default=0), and 1 represents 0/1 coding. flag1=1 is the same as –1 flag in plink. Please see the plink manual. |
File_Cov |
an input file name of plink covariates file. The first two columns of this file should be FID and IID. |
cov_header |
a logical value indicating whether the covariate file contains a header row (default=TRUE) |
A dataframe of Family ID (FID), Individual ID (IID), Paternal ID (PID), Maternal ID(MID), Sex, and Phenotype. If Read_Plink_FAM_Cov is used with a covariate file, the dataframe has covariates from the 7th column.
Seunggeun Lee
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