I'm trying to use signeR to assess mutation signatures in a particular signature, but I keep getting the following error:
vcfobj <- readVcf("D:\R\UTSW.SNV.vcf", "hg19") mut <- genCountMatrixFromVcf(mygenome,vcfobj) opp <- genOpportunityFromGenome(mygenome, target_regions, nsamples=nrow(mut)) signatures <- signeR(M=mut, Opport=opp, nlim=c(2,11)) Evaluating models with the number of signatures ranging from 2 to 11, please be patient. Evaluating 2 signatures. EM algorithm: |==================================================================| 100% Running Gibbs sampler for 2 signatures...Error in apply(E, 1, function(v) { : dim(X) must have a positive length In addition: Warning messages: 1: In validityMethod(object) : Dimensions of W and H look strange [ncol(W)= 2 > ncol(H)= 1 ] 2: In validityMethod(object) : Dimensions of W and H look strange [ncol(W)= 2 > ncol(H)= 1 ] 3: In validityMethod(object) : Dimensions of W and H look strange [ncol(W)= 2 > ncol(H)= 1 ]
Here are the matrices that I'm using:
mut C>A:ACA C>A:ACC C>A:ACG C>A:ACT C>A:CCA C>A:CCC C>A:CCG C>A:CCT UTSWSNV 114 102 27 109 172 165 36 204 C>A:GCA C>A:GCC C>A:GCG C>A:GCT C>A:TCA C>A:TCC C>A:TCG C>A:TCT UTSWSNV 55 55 8 97 116 188 20 165 C>G:ACA C>G:ACC C>G:ACG C>G:ACT C>G:CCA C>G:CCC C>G:CCG C>G:CCT UTSWSNV 28 19 2 18 34 29 5 21 C>G:GCA C>G:GCC C>G:GCG C>G:GCT C>G:TCA C>G:TCC C>G:TCG C>G:TCT UTSWSNV 17 14 4 13 38 26 2 29 C>T:ACA C>T:ACC C>T:ACG C>T:ACT C>T:CCA C>T:CCC C>T:CCG C>T:CCT UTSWSNV 114 75 66 89 139 94 74 102 C>T:GCA C>T:GCC C>T:GCG C>T:GCT C>T:TCA C>T:TCC C>T:TCG C>T:TCT UTSWSNV 202 175 89 155 116 81 24 79 T>A:ATA T>A:ATC T>A:ATG T>A:ATT T>A:CTA T>A:CTC T>A:CTG T>A:CTT UTSWSNV 87 79 94 102 58 91 111 102 T>A:GTA T>A:GTC T>A:GTG T>A:GTT T>A:TTA T>A:TTC T>A:TTG T>A:TTT UTSWSNV 72 66 127 94 126 119 94 207 T>C:ATA T>C:ATC T>C:ATG T>C:ATT T>C:CTA T>C:CTC T>C:CTG T>C:CTT UTSWSNV 72 99 132 82 87 183 231 126 T>C:GTA T>C:GTC T>C:GTG T>C:GTT T>C:TTA T>C:TTC T>C:TTG T>C:TTT UTSWSNV 81 119 111 58 92 122 111 115 T>G:ATA T>G:ATC T>G:ATG T>G:ATT T>G:CTA T>G:CTC T>G:CTG T>G:CTT UTSWSNV 12 9 17 19 9 9 26 19 T>G:GTA T>G:GTC T>G:GTG T>G:GTT T>G:TTA T>G:TTC T>G:TTG T>G:TTT UTSWSNV 11 8 21 12 13 5 13 24 opp C>A:ACA C>A:ACC C>A:ACG C>A:ACT C>A:CCA C>A:CCC C>A:CCG C>A:CCT [1,] 1472 960 307 1251 1495 1177 371 1438 C>A:GCA C>A:GCC C>A:GCG C>A:GCT C>A:TCA C>A:TCC C>A:TCG C>A:TCT [1,] 1162 1067 321 1133 1485 1278 217 1590 C>G:ACA C>G:ACC C>G:ACG C>G:ACT C>G:CCA C>G:CCC C>G:CCG C>G:CCT [1,] 1472 960 307 1251 1495 1177 371 1438 C>G:GCA C>G:GCC C>G:GCG C>G:GCT C>G:TCA C>G:TCC C>G:TCG C>G:TCT [1,] 1162 1067 321 1133 1485 1278 217 1590 C>T:ACA C>T:ACC C>T:ACG C>T:ACT C>T:CCA C>T:CCC C>T:CCG C>T:CCT [1,] 1472 960 307 1251 1495 1177 371 1438 C>T:GCA C>T:GCC C>T:GCG C>T:GCT C>T:TCA C>T:TCC C>T:TCG C>T:TCT [1,] 1162 1067 321 1133 1485 1278 217 1590 T>A:ATA T>A:ATC T>A:ATG T>A:ATT T>A:CTA T>A:CTC T>A:CTG T>A:CTT [1,] 1331 1005 1369 1698 902 1348 1683 1481 T>A:GTA T>A:GTC T>A:GTG T>A:GTT T>A:TTA T>A:TTC T>A:TTG T>A:TTT [1,] 919 775 1199 1098 1477 1444 1356 2634 T>C:ATA T>C:ATC T>C:ATG T>C:ATT T>C:CTA T>C:CTC T>C:CTG T>C:CTT [1,] 1331 1005 1369 1698 902 1348 1683 1481 T>C:GTA T>C:GTC T>C:GTG T>C:GTT T>C:TTA T>C:TTC T>C:TTG T>C:TTT [1,] 919 775 1199 1098 1477 1444 1356 2634 T>G:ATA T>G:ATC T>G:ATG T>G:ATT T>G:CTA T>G:CTC T>G:CTG T>G:CTT [1,] 1331 1005 1369 1698 902 1348 1683 1481 T>G:GTA T>G:GTC T>G:GTG T>G:GTT T>G:TTA T>G:TTC T>G:TTG T>G:TTT [1,] 919 775 1199 1098 1477 1444 1356 2634
Does anyone see any glaring errors here?
Thanks
