[BioC] crlmm - computeCopynumber error

[Christian Ruckert]

I get an error for some chromosomes when running function

computeCopynumber(chrom=i, A=A, B=B, calls=genotypes, conf=conf, NP=NP, 
plate=plate, envir=env, DF.PRIOR=50, MIN.OBS=1, SNR=SNR, SNRmin=SNRmin)

from package crlmm. The output is:

Sufficient statistics
.
Estimating coefficients
.
Allele specific copy number
.
Copy number for nonpolymorphic probes...
.Error in crossprod(X[ix, ]) : object 'ix' not found


The error origins in function nonpolymorphic in lines

if (nrow(X) > 5000)
         ix <- sample(1:nrow(X), 5000)
     betahat <- solve(crossprod(X[ix, ]), crossprod(X[ix, ], Y[ix]))

It seems, that ix is not initialized if nrow(X) < 5000.


Regards,
Christian