Loading sqlite database file onto RStudio

[karthikajith]

Hi!

I have been trying to load an sqlite file from Galaxy onto RStudio, for a cummerbund script, but it doesnt work.

This is the error that I keep getting on RStudio-

cuff_data ← readCufflinks(“FILE”)
Creating database FILE/cuffData.db
Error: Could not connect to database:
unable to open database file

I tried a couple a couple different things. I’m not too tech savvy.
Any help would be sincerely appreciated. Thank you!

[jennaj]

Welcome @karthikajith

To get the data into the R environment from Galaxy, you’ll need to use the gx_get() command.

This is a good earlier topic with an example:

@dadrasarmin

As already mentioned here, the function gx_get() just returns a path to a file for you. It does not read a table for you.

How can you import your file?
Let’s say you want to import your tsv table which is dataset number 7 in your current history as RStudio. You can get the path as follows:

table <- read.table(gx_get(7), header=T, sep="\t", row.names = 1)

Of course, you can also do it differently such as:

path <- gx_get(7)
table <- read.table(path, header=T, sep="\t", row.names = 1)

It is important to understand that gx_get() returns just a path and do not transfer any file.

We also have some tutorials for this at the GTN.

• GTN Tutorials for RStudio
• Then, a search will bring up FAQs too GTN Materials Search (query=rstudio)

Please give this method a try, thanks!