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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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Error: argument 'x' contains missing values #35

Closed Deeptirao closed 3 years ago

Deeptirao commented 4 years ago

Please help me in resolving the error of missing values for x, which is not allowing me to calculate G prime.

df_filt <- runGprimeAnalysis(

  • SNPset = df_filt,
  • windowSize = 1e6,
  • outlierFilter = "deltaSNP") 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: argument 'x' contains missing values

My file looks like this:

head(df_filt) CHROM POS REF ALT AD_REF.LOW AD_ALT.LOW DP.LOW GQ.LOW PL.LOW SNPindex.LOW AD_REF.HIGH AD_ALT.HIGH DP.HIGH 1 Chr1 1058 T TA 28 18 46 NA NA 0.3913043 41 17 58 2 Chr1 2541 T TC 31 4 35 NA NA 0.1142857 25 2 27 3 Chr1 2559 CTAGG ATAGT,CTAGT 32 10 42 NA NA 0.2380952 28 9 37 4 Chr1 2627 GCTTC ACTCT,ACGTC,GCTCC 41 18 59 NA NA 0.3050847 NA NA 40 5 Chr1 2653 C T 33 31 64 NA NA 0.4843750 29 13 42 6 Chr1 2722 ATTTTTTTTGAG ATTTTTTTTTAAG,ATTTTTTTTAAA NA NA 57 NA NA NA 24 15 39 GQ.HIGH PL.HIGH SNPindex.HIGH REF_FRQ deltaSNP nSNPs tricubeDeltaSNP minDP tricubeDP CI_95 CI_99 1 NA NA 0.29310345 0.6634615 -0.098200900 619 -0.009587027 46 30 -0.4333333 -0.5333333 2 NA NA 0.07407407 0.9032258 -0.040211640 622 -0.009638414 27 30 -0.4333333 -0.5333333 3 NA NA 0.24324324 0.7594937 0.005148005 622 -0.009639038 37 30 -0.4333333 -0.5333333 4 NA NA NA NA NA 622 -0.009641394 40 30 -0.4333333 -0.5333333 5 NA NA 0.30952381 0.5849057 -0.174851190 622 -0.009642295 42 30 -0.4333333 -0.5333333 6 NA NA 0.38461538 NA NA 622 -0.009644686 39 30 -0.4333333 -0.5333333

bmansfeld commented 4 years ago

Hi sorry for the delayed response. Seems like you have lots of NA missing values in your dataset. Try filtering out INDELS before importing into qtlseqr that may be the problem (though it shouldn't really)