Hi,
i tried to find the answer but didn't so my apologies if the question is
obvious !
I'm trying to parallelize the following R code :
pk2test =
c(1:16,(12*16+1):(12*16+16),(16*16+1):(16*16+16),(20*16+1):(20*16+16))
score.mat = matrix(nc=16*4,nr=16*4)
for(i in 1:(16*4)) {
for(j in i:(16*4)) {
score.mat[i,j] = score.mat[j,i] =
computeScore(pk[[pk2test[i]]],pk[[pk2test[j]]],10,5)$score
}
}
pk is a list of Object of type MassPeak from MALDIquant library. Each
object is composed with a mass vector (@mass) an intensity vector
(@intensity) and a metaData field (another list)
score.mat is a matrix with scores (reals)
pk2test is just a vector to know which objects in pk i want to deal with
computeScore is the function i wrote to compute the score, it calls
another function called filterSpectra
I write the function like that, and i got the error below, and i can't
figure out why ?
pk2test =
c(1:16,(12*16+1):(12*16+16),(16*16+1):(16*16+16),(21*16+1):(21*16+16))
score.mat = matrix(nc=16*4,nr=16*4)
for(i in 1:4) {
score.mat[i,i:4] =
foreach(filterSpectra=filterSpectra,
computeScore=computeScore,
pk=pk,pk2test=pk2test,i=i,j=c(i:4),
.combine="c", .packages="MALDIquant" ) %dopar% {
computeScore(pk[[pk2test[i]]],pk[[pk2test[j]]],10,5)$score
}
}
Error: trying to get slot "mass" from an object of a basic class
("integer") with no slots.
I think it is because when parallelizing, object are sent to child R
session, but i don't understand how i have to write things to get it work.
If someone have a clue, it would be really appreciated and would let me
save a lot of computing time !!
Thanks in advance,
Julien
--
Envoyé de mon ENIAC
Julien Textoris
CCA - Service d'anesthésie et de réanimation
Hôpital Nord, Assistance Publique - Hôpitaux de Marseille
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13915 Marseille
+33 491 965 531
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