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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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"runGprimeAnalysis" cannot work well #11

Closed xuxuda closed 5 years ago

xuxuda commented 5 years ago

QTLseq analysis can be successfully runned and get the good QTL analysis plots. Howerver, when I try to extract significant regions using "getSigRegions", I was told the following warnings: "Error in**getSigRegions(SNPset = df_filt, alpha = 0.01) : Please first use runGprimeAnalysis to calculate q-values". Thus, I run "> df_filt <- runGprimeAnalysis(SNPset = df_filt, windowSize = 2e8, outlierFilter = "deltaSNP")"** Then more warnings coming.........

Counting SNPs in each window... Calculating tricube smoothed delta SNP index... Calculating G and G' statistics... Using deltaSNP-index to filter outlier regions with a threshold of 0.1 Estimating the mode of a trimmed G prime set using the 'modeest' package... Error in mutate_impl(.data, dots) : Evaluation error: $ operator is invalid for atomic vectors. May you give me some advices ?

bmansfeld commented 5 years ago

Thanks for the comments. If you want significant regions for QTLseq please set the method = "QTLseq" in getSigRegions(). Also make sure to set the interval parameter. See ?getSigRegions for help.

In regard to the Gprime errors. I am aware of this bug due to a recent change in the modeest package. Thanks for flagging this. I will fix it this weekend, for now you can downgrade modeest to version 2.1 and it should work. Thanks again, Ben

xuxuda commented 5 years ago

Thanks for your reply! It actually is the problem of the "modeest" package but I fail to fix it. Waiting for you to fix the bug. Best wishes!

Dengan

bmansfeld commented 5 years ago

Ok this has been fixed in QTLseqr v0.7.4. Good luck with your work!