How to convert large gene counts data into matrix?
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@sambunga094-21466
Last seen 3.2 years ago

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

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 singlecell bioinformatics seurat • 2.9k views