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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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Issue with CI names #57

Closed cheesemania closed 1 year ago

cheesemania commented 1 year ago

Hi, great tool!

I can run G prime analysis absolutely fine, but I get an issue with the deltaSNP analysis around the CI simulations. Can you shed any light on whats going on?

Thanks

Ian

df_filt<-runQTLseqAnalysis(dffilt,bulkSize=100,windowSize=200000,filter=0.1) Counting SNPs in each window... Calculating tricube smoothed delta SNP index... Returning the following two sided confidence intervals: 95, 99 Variable 'depth' not defined, using min and max depth from data: 150-150 Assuming bulks selected from F2 population, with 100 individuals per bulk. The 'bulkSize' argument is of length 1, setting number of individuals in both bulks to: 100 Simulating 10000 SNPs with reads at each depth: 150-150 Keeping SNPs with >= 0.1 SNP-index in both simulated bulks Error in names(CI) <- paste0("CI", 100 - (intervals * 200)) : 'names' attribute [2] must be the same length as the vector [1]

bmansfeld commented 1 year ago

Hey, I'm not sure what's going on, but I'm guessing it has something to do with the fact the the min and max depth are equal (150). That's kinda funny? did you filter the data to only include SNPs of that depth? alternatively play around with the filter perimeter? does changing that impact running? Let me know if that helps, otherwise ill need to see df_filt to see if I can debug. Ben