I have imputed dataset from IMPUTE2, including .info, .info_by_sample, and .txt.gz (contains the genotype data) files. I would like to know how I can convert these data files into the .mlinfo and .mldose files. I tried to use the package in R (DatABEL) to convert the .txt.gz file into the filevector format. After 20 minutes, it gave me an error as:
Code: Select all
Error in (function (cl, name, valueClass) :
assignment of an object of class “NULL” is not valid for @‘data’ in an object of class “databel”; is(value, "externalptr") is not TRUE
I am wondering if there are other tools that I can use to generate the .mldoes files. Moreover, I would like to know how to generate the .mlinfo file from the IMPUTE2 data.I assume that the "info" in IMPUTE2 corresponds to the "Rsq" in .mlinfo and "certainty" in IMPUTE2 corresponds to the "Quality" in .mlinfo. However, I don't know where I can find the allele information (A1, A2).
Thank you so much!