purity and mafR.clust NA

[solivehong]

hi I used this software to analyze my own tumor samples，Bam from ffpe sample for lung cancer panal detection

rcmat = readSnpMatrix(data) xx = preProcSample(rcmat) oo=procSample(xx,cval=150,min.nhet = 15) fit=emcncf(oo) Warning message: In max(mafR.clust[seg$chrom < nX & seg$nhet > min.nhet], na.rm = T) : no non-missing arguments to max; returning -Inf oo$dipLogR [1] 0.05316949 head(fit$cncf) chrom seg num.mark nhet cnlr.median mafR segclust cnlr.median.clust 1 1 1 1201 0 -0.07673154 0.000000000 22 -0.07968007 2 2 2 150 0 0.18639063 0.000000000 26 0.16282653 3 2 3 11 0 -1.48396998 0.000000000 9 -1.46912981 4 2 4 152 1 0.45479562 0.031159799 31 0.44356851 5 2 5 26 0 -1.68720643 0.000000000 8 -1.68720643 6 2 6 268 1 0.36159392 -0.005017797 30 0.37677684 mafR.clust start end cf.em tcn.em lcn.em 1 NA 658000 244006600 0.3 1 0 2 NA 173315 39239542 0.3 3 NA 3 NA 39240700 39251371 0.3 0 0 4 NA 39261800 48066810 0.3 4 NA 5 NA 52798272 58459300 0.3 0 0 6 NA 58468500 109375137 0.3 4 NA

Is there a problem with my sample or with my parameter settings? I'm a biological beginner who wants to answer a detailed point.

[veseshan]

Your sample seems to have hardly any het SNPs. The numbers in the nhet column above are zero or 1. In a typical WES sample one would expect 8-10% hets. This could either be due to the way the panel was designed or you have genome build mismatch in the analysis.

[kobejamescurry]

This could either be due to the way the panel was designed so have you tested any panel data, what is "the way" you refer to, thanks a lot.