Comments (5)
Hi,
this is a known issue, for some reason nmf function loaded via namespace gives this error.
try manually loading NMF package before running extractSignatures. It should work fine.
library('NMF')
AP1.hg19.sign = extractSignatures(mat = AP1.hg19.tnm)
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Thanks James
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Im getting a similar error even after loading the NMF library. Is there is any other obvious fix to this?
Thanks,
Teja
library('NMF')
laml.sign = extractSignatures(mat = laml.tnm)
Warning : Found zero mutations for conversions T[T>G]C
Estimating best rank..
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> attempt to set 'rownames' on an object with no dimensions [in call to 'rownames<-']
-#2 [r=3] -> attempt to set 'rownames' on an object with no dimensions [in call to 'rownames<-']
-#3 [r=4] -> attempt to set 'rownames' on an object with no dimensions [in call to 'rownames<-']
-#4 [r=5] -> attempt to set 'rownames' on an object with no dimensions [in call to 'rownames<-']
-#5 [r=6] -> attempt to set 'rownames' on an object with no dimensions [in call to 'rownames<-']
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I worked out on this by specifying exact values of n. I think because my mutation data were not large enough to run the default n parameter and find the best signature.
So I ran n=1 to n=5 separately and chose signature with the highest correlation as described in the manual. I noticed that the same error came up again when you used large n.
My command:
library('NMF')
install.extras('NMF')
A = trinucleotideMatrix(maf = AP, ref_genome = 'hg19_chromosome.fa', prefix = 'chr', add = TRUE, ignoreChr = 'chrM', useSyn = TRUE)
A2 = extractSignatures(mat = A, n = 1, plotBestFitRes = T)
A2 = extractSignatures(mat = A, n = 2, plotBestFitRes = T)
...
A2 = extractSignatures(mat = A, n = 6, plotBestFitRes = T)
plotSignatures(A2)
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Thanks @wjaratlerdsiri. That worked!
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