How to import huge .csv files in R studio?
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4.4 years ago
krushnach80 ▴ 900

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 ?

R RNA-Seq • 29k views
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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

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8
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4.4 years ago

fread() from data.table package is blazing fast for reading large files. 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 using as.data.frame(x) or by using data.table=FALSE in the argument of fread().

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6
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4.4 years ago

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.

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4.4 years ago
sm30 ▴ 40

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

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yes finally I used that library

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