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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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getQTLTable without running runGprimeAnalysis #41

Closed liufy11 closed 3 years ago

liufy11 commented 3 years ago

Hello, To my knowledge , runGprimeAnalysis and runQTLseqAnalysis are two seperate function. after running runQTLseqAnalysis, I want to get QTL region using getQTLTable, but the screen says "Error in getQTLTable(SNPset = df_filt, alpha = 0.01, interval = 99.9999999, : Please first use runGprimeAnalysis to calculate q-values".

Can't I only use runQTLseqAnalysis and get the QTL region ?

If I run runGprimeAnalysis and then run runQTLseqAnalysis , which is the result comes from ? runGprimeAnalysis or runQTLseqAnalysis

bmansfeld commented 3 years ago

Hi, the default method parameter for getQTLTable() is method = "Gprime". So when you didn't include that argument when you ran the code it defaults to that. Set method = "QTLseq" to get those results. Good luck! Ben