I would greatly appreciate any help with this, and I apologise if it is really simple.
I am trying to use the --make-pheno command in plink to convert my phenotype text file to a phenotype file so that I can use this in subsequent analysis
The format of the phenotype.txt at present is in a unix txt tab delimited file The first few lines are as follows:
FID IID MN p_pos s_pos a_pos MN001CORCON MN001CORCON 2 -9 -9 -9 MNBEL02013012015P MNBEL02013012015P 2 1 1 -9 MNBRA01102082014P MNBRA01102082014P 2 2 1 -9 MNCAM0051922014PMP MNCAM0051922014PMP 2 1 1 -9
I have also tried converting column 3 to the default of * to signify case However I keep coming up with errors I have tried entering the value for cases in quotation marks like '*' which has not worked
The command I am entering is:
plink2 --make-pheno phenotype.txt '2'
My output is: Options in effect: --make-pheno mnpppht2.txt 2
Error: No input dataset.
I have also tried this:
plink --bfile filename --make-pheno phenotype.txt 2 --make-bed --out newfilename
But got this error for the phenotype data from - output: --make-pheno: 0 phenotype values set.
Any help would be very much appreciated as I need to have a functioning phenotype file in order to do further data analysis.
Thank you very much Sanjana