Question: How to import huge .csv files in R studio?
0
gravatar for krushnach80
10 months ago by
krushnach80160
krushnach80160 wrote:

I want to import an expression .csv file in R studio ,but the size limit is 5 mb max my file is 30 mb how do I do that?

The file is mrna seq data from TCGA which I want to extract.How can I do that is there any way to import the huge file and see ?

rna-seq R • 1.1k views
ADD COMMENTlink modified 10 months ago by Ron600 • written 10 months ago by krushnach80160

I think you may use ff lib

library(ff)

your_data <- read.csv.ffdf(file = 'your_file.csv', header = T)

other solution use bigmemory

the authors successfully load a CSV with size as large as 11GB

more details and other solution could be found here

ADD REPLYlink modified 10 months ago • written 10 months ago by Medhat6.9k
5
gravatar for Devon Ryan
10 months ago by
Devon Ryan70k
Freiburg, Germany
Devon Ryan70k wrote:

Try using read.csv() rather than clicking on files. The limitation is there to prevent you from trying to edit large files, which will degrade performance significantly.

ADD COMMENTlink written 10 months ago by Devon Ryan70k
2
gravatar for Santosh Anand
10 months ago by
Santosh Anand2.9k
Santosh Anand2.9k wrote:

fread() from data.table package is blazing fast for reading large file. It tries to guess the delimiter and header automatically. It will give you an object of class "data.table", which is very similar to data.frame though quirky sometimes. You can easily convert it to your familiar data.frame by as.data.frame(x).

ADD COMMENTlink written 10 months ago by Santosh Anand2.9k
2
gravatar for sm30
10 months ago by
sm3020
sm3020 wrote:

CRAN pakage TCGA2STAT can be used to directly import TCGA data into R.

ADD COMMENTlink written 10 months ago by sm3020

yes finally I used that library

ADD REPLYlink written 10 months ago by krushnach80160
2
gravatar for Ron
10 months ago by
Ron600
United States
Ron600 wrote:

http://stackoverflow.com/questions/1727772/quickly-reading-very-large-tables-as-dataframes-in-r

read.csv.sql() from https://cran.r-project.org/web/packages/sqldf/sqldf.pdf

ADD COMMENTlink written 10 months ago by Ron600
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