hello everyone!
recently, I read the paper "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data".
I tried many times to use the R package CENTIPEDE, but I did not figure out what its input file should be.
reading its example, I think the input file should be looked like below.
the 1st file a , every row contains a vector of read counts
0 0 0 1 0 3 ..... 0 0 2 4 0 1
the 2nd file b , like this:
chr1 90336 90356 - 16.69222 0.03875 31393
but when i run THE command:
centFit <- fitCentipede(Xlist = list(DNase=as.matrix(a)), Y=cbind(rep(1, dim(b)[1]), b[,5], b[,6]))
there was an error:
Error in if (B1 > 0.999999) { : missing value where TRUE/FALSE needed
I did not know why.
can anybody help me ?
thanks!
recently, I read the paper "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data".
I tried many times to use the R package CENTIPEDE, but I did not figure out what its input file should be.
reading its example, I think the input file should be looked like below.
the 1st file a , every row contains a vector of read counts
0 0 0 1 0 3 ..... 0 0 2 4 0 1
the 2nd file b , like this:
chr1 90336 90356 - 16.69222 0.03875 31393
but when i run THE command:
centFit <- fitCentipede(Xlist = list(DNase=as.matrix(a)), Y=cbind(rep(1, dim(b)[1]), b[,5], b[,6]))
there was an error:
Error in if (B1 > 0.999999) { : missing value where TRUE/FALSE needed
I did not know why.
can anybody help me ?
thanks!
