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molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
https://github.com/molgenis/systemsgenetics/wiki
GNU General Public License v3.0
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Decon-eQTL - dosage file missing values #589

Closed mooreann closed 3 years ago

mooreann commented 3 years ago

Is Decon-eQTL equipped to deal with dosage genotype files that are missing values? If so, what should missing values be? Or will I be required to just drop the SNPs with any missing values?

Currently I have tried replacing missing values with empty string and 'NA' strings and have gotten similar errors:

Exception in thread "main" java.lang.NumberFormatException: For input string: "NA" at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at main.java.decon_eQTL.Utils.StringVectorToDoubleArrayList(Utils.java:133) at main.java.decon_eQTL.GenotypeData.(GenotypeData.java:38) at main.java.decon_eQTL.Deconvolution.readInputData(Deconvolution.java:47) at main.java.decon_eQTL.Main.main(Main.java:24)

npklein commented 3 years ago

I released a new version (v1.4, Decon-eQTL-v1.4-jar-with-dependencies.jar) that should be able to handle missing genotypes.

The missing genotypes should be encoded as -1.