How to download data in a format that allows easy tranfer to R

Q&A
1

I am working on downloading the CCLE_RNAseq_reads and getting this data into a R dataframe to work with. This is not easy since the file is huge and has a massive number of columns.

Can you get all of the data from a .txt file to an R dataframe? If this is not good, how do you download the data from ccle in a format that can be imported into R?

2

R should be capable of easily handling quiet large csv files such as CCLE_RNAseq_reads.csv.

Specifically, R’s read.csv function ( Reading and Writing CSV Files – Programming with R ) should have no problem reading the CCLE_RNAseq_reads.csv file.

That function should work fine, but it is a little slow. For large files, I believe the data.tables package provides a readf function which is much faster.

I just tried the following and it appears to work (takes about 5-10 seconds on my laptop)

> df <- data.table::fread("CCLE_RNAseq_reads.csv")

Thanks,
Phil

3

Thanks very much. I will try this. I’m not sure what the issue is, but my RStudio says the memory limit is 5 MB.

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