How to convert large gene counts data into matrix?
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@sambunga094-21466
Last seen 4.7 years ago

Hi, I have a gene counts table which something looks like this:

enter image description here

When i'm trying to convert this into a matrix im getting this following error:

Error in asMethod(object) : 
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105`

This is the code that i'm using which i borrowed from a tutorial online:

library(Matrix)
library(data.table)
f<-as.data.frame(fread(file="Z:/sc_wizard/data.counts",h=T,sep='\t'))
sm = sparseMatrix(as.numeric(factor(f$gene)), as.numeric(factor(f$cell)), x=f$count)
rownames(sm)<-levels(factor(f$gene))
colnames(sm)<-levels(factor(f$cell))
write.table(as.matrix(sm),file = "out.tsv",sep='\t',col.names=T,row.names=T,quote=F)`

Help is really appreciated. Thank you!!

R Bioconductor singlecell bioinformatics seurat • 3.7k views
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