faster way to run a loop in r -


i have 3 dataframes a,b , c.

a has 18000 rows , 18000 columns , b has 150000 rows , 5 cols.

i want fill elements of b.

the loop take long time. how can run loop faster?

example of 

entrez_gene_id 2324 34345 4345 1234 3453 1 entrez_gene_id    0     0    0    0    0 2          23040    0     0    0    0    0 3           7249    0     0    0    0    0 4          64478    0     0    0    0    0 5           4928    0     0    0    0    0 6          58191    0     0    0    0    0

example of b

  head(b)   v1 gene1 gene2      weight   newweight 1  1  4171  4172  2.01676494 0.020420929 2  2  2237  5111 1.933298567 0.015300857 3  4   506   509 2.439170425 0.020577243 4  7  6635  6636 2.255316779 0.081088975 5  8  6133  6210 3.427969232 0.021132906 6 10 23521  6217 1.607247743 0.027792961

and code : 

b<- data.frame(lapply(c, as.character), stringsasfactors=false)  for(i in 1:nrow(b)){   rname=b[i,2]   cname=b[i,3]   a[rname,cname]=b[i,5]   print(i) }

it seems though trying fill full matrix matrix in sparse notation. can use dgcmatrix class matrix package this:

library(matrix) b_mat <- sparsematrix(i=b[,2],j=b[,3],x=b[,5])

this leaves matrix in sparse format. convert 18,000 x 18,000 form:

as.data.frame(as.matrix(b_mat))

edit: suggest leaving as.data.frame call out here, matrix easier work considering number of columns have


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