Data formats

There are three ways to handle input data with Haplin:

  1. The native Haplin data file format is a  fairly simple ASCII file, described here.

  2. If the data (on relatively few SNPs) are available in a standard ped-format, it is possible to convert ped files directly to the Haplin format. See here for details.

  3. With a larger number of SNPs in ped-format, such as a GWAS ped file produced by PLINK, data can be read into Haplin using the ff package. This approach has been designed by Julia Romanowska and is described in this vignette: B_Reading_data.

    NOTE: Prior to version 7.0.0, Haplin used the data format of the GenABEL package, with additional accomodations for family data. Regrettably, GenABEL was abandoned rather abruptly, and consequently files in the old format are not accessible the way they used to be. Possibly, a Haplin version prior to 7.0.0 combined with an archived version of GenABEL might conveivably still work, although we have not tried this.

    A more detailed description of the other Haplin data formats as well as the abandoned GenABEL format can still be found here.