I apologise because I know this question has been asked before, but I've tried most variations of the answer to no help.
I am using the foreach package to run a loop of the NMF algorithm on a set of data. I am them trying to extract the set of basis names using the ExtractFeatures function, which outputs each run as a list of how many ranks you determine (in the example I have, 3).
Here is my code below (I've used a sample dataset from the NMF Vignette):
library("NMF")
library("doParallel")
library("foreach")
#load vignette dataset and shorten it for time's sake
data(esGolub)
esGolub <- esGolub[1:200,]
#output matrix
Extract_Genes <- matrix()
#set cores
registerDoParallel(cores = 3)
#Loop NMF runs and extract features
foreach(i =1:4, .packages = "NMF") %dopar%{
i <- nmf(esGolub, 3, nrun = 1)
Extract_Genes <- extractFeatures(i, format = "list")
}
This outputs the list of extracted genes like so:
[[1]]
[[1]][[1]]
[1] 43 120 128 130
[[1]][[2]]
[1] 94 1 112 42 8 64 96 182 59 41 69 25 26
[[1]][[3]]
[1] 39 74 2 91 190 167 103 129 174
3 times over for the 3 runs, but it does not save. Would anyone have any suggestions on how I save these outputs?
Thank you in Advance, J
Comment by Imo works fine:
myList <- foreach(i =1:4, .packages = "NMF") %dopar%{