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


Comments

Post a Comment

Popular posts from this blog

javascript - jQuery: Add class depending on URL in the best way -

i have html progress meter: <div class="col-md-3" style="margin-left: -20px;"> <div class="progress-pos active" id="progess-1"> <div class="progress-pos-inner"> login </div> </div> </div> <div class="col-md-3 progress-pos-container"> <div class="progress-pos" id="progess-2"> <div class="progress-pos-inner"> scan items </div> </div> </div> <div class="col-md-3 progress-pos-container"> <div class="progress-pos" id="progess-3"> <div class="progress-pos-inner"> confirm address </div> </div> </div> <div class="col-md-3 progress-pos-container"> <div class="progress-pos" id="progess-4"> <div class="progress-pos-in...
Read more

caching - How to check if a url path exists in the service worker cache -

i need check if particular url path exists in service worker cache. example, suppose url is: /myserviceworker/service?a=110&b=70 this url exists in cache, there many of them different values of , b. now, suppose want refresh of these urls, how can that? i want know how access key values service worker cache. if know key, plan follows: var url = new url(key); if(url.pathname === "\/myserviceworker/service") refetch key but not sure how cache key , in format is. mean, string or url? cache api has match() method returns promise resolving in response object if match or undefined if no match exists. second parameter object can specify ignoresearch not take account url parameters. the ignoresearch option supported firefox ( chrome status here ). in other hand, retrieve cache entries, can use keys() method.
Read more

Redirect to a HTTPS version using .htaccess -

i need modify .htaccess file redirect urls https version without "www". http://example.com --> https://example.com http://www.example.com --> https://example.com https://www.example.com --> https://example.com this how .htaccess file looks like: rewriteengine on rewritecond %{request_filename} !-d rewritecond %{request_filename} !-f rewriterule ^(.*)$ redirect.php?id=$1&page=$2 [qsa,l] what modifications need make .htaccess in order forward https without "www"? it depends on doing current code. looks file called redirect trying display php page seo friendly url. think might confusing people. anyway, need , force https without www, need 1 more rule above. also second rule needs two capture groups in rewriterule test string because wanting 2 different values using $1 , $2 references. rewriteengine on #rediect www non www and/or http https --- combinations. rewritecond %{http_host} !^example\.com [nc,or] rewritecond %{https} !^...
Read more