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UW-GAC / GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
https://bioconductor.org/packages/GENESIS
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Error using assocTestAggregate #105

Open pjuge opened 11 months ago

pjuge commented 11 months ago

Hi,

I am using the GENESIS package to perform a SKAT-O analysis on every chromosome, variants being aggregated by genes. I am using the same code for all of the chromosomes, and it worked perfectly until the chromosome 19.

Running the code

assoc <- assocTestAggregate(iterator,
+                             mod_1,
+                             test="SKATO",
+                             AF.max=0.01,
+                             weight.beta=c(1,25),
+                             verbose = FALSE)

I have the following message: Error in seqBlockApply(gdsobj, "genotype", function(x) { : Invalid position in CIndex.

I can provide more details if needed. Thanks!

smgogarten commented 11 months ago

It sounds like the code is looking for a position that doesn't exist in the genotype file. I can't tell you more than that without seeing the actual data file, but I suggest creating an iterator object just for chrom 19 with the same genes you're using in your analysis and trying to do a simple task with it (maybe printing out the number of variants?), so you can see on what region it's failing.