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magnusdv / forrel

Forensic pedigree analysis and relatedness inference
GNU General Public License v2.0
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Read frequency database on Familias and FamLinkX format #28

Closed thoree closed 4 years ago

thoree commented 4 years ago

It would be nice to be able read tab separated asci files exported from Windows Familias and FamLinkX on the below format to define ped markers

DXS10148 13.3 0.4 14 0.3 17 0.3

DXS10135 16 0.5 16.1 0.5 ...

knifecake commented 4 years ago

I believe there is a function inside the epGUI code that does this, namely attachAlleleFrequenciesToPedigree.familias. It takes a pedigree ped and a file path path and attaches the frequency data found in the file at path to the pedigree ped. I tested it with the sample files that @thoree provided for epGUI and it appeared to work fine.

Something we could do is move just this function to the main forrel branch so that it is available even though the epGUI is still not ready. I can create a new branch and incorporate this function to say R/readFam.R.

Here is the link to the file that contains the function: https://github.com/magnusdv/forrel/blob/shiny-gui/inst/exclusionPowerUI/importAdapters/familias-import-adapter.R#L20

magnusdv commented 4 years ago

This functionality is now implemented in pedtools::readFrequencyDatabase().