R memory problem with sparseMatrix/as.matrix

General
1

Hi,

I have a text file from which I want to create a sparse Matrix. I do is as the following and a sparse matrix is created:

My data looks like the following:

a <- read.csv("h3k_test_chr1.txt", sep ="\t", header = TRUE)
head(a)
       x1      y1    z1
1 2500000 2500000  7091
2 2500000 5000000  2465
3 5000000 5000000 10244
4 2500000 7500000  1214
5 5000000 7500000  2638
6 7500000 7500000  8958

Z <- sparseMatrix(i = a$x1 , j = a$y1, x = a$z1, symmetric = TRUE)

But when I run as.matrix(Z), I get the following error:

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

I would appreciate if you can guide me how to get rid of the above error, is it memory related?

Thank you
Best,
Karni Bedirian

2

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