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ctlab / fgsea

Fast Gene Set Enrichment Analysis
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Loading own data #37

Closed PaulineMarangoni closed 5 years ago

PaulineMarangoni commented 5 years ago

Hi there,

I have been trying to explore your vignette and now wanted to try applying the same workflow to my own pre-ranked files. However, I keep getting the same error reported regarding my rnk file

> rnk.file <- system.file("extdata", "Cluster11_GSEA.rnk", package="fgsea") > ranks <- read.table(rnk.file, header = TRUE, colClasses = c("character", "numeric")) Error in read.table(rnk.file, header = TRUE, colClasses = c("character", : no lines available in input In addition: Warning message: In file(file, "rt") : file("") only supports open = "w+" and open = "w+b": using the former

I not sure the rnk file was formatted properly, but also not sure about calling the functions exactly how I am supposed to. Any help you could provide on this matter would be highly appreciated.

Thanks!

assaron commented 5 years ago

rnk.file should the full path to the file with ranks, "Cluster11_GSEA.rnk". Don't use system.file call, it is just to get the example file coming with the package.

rnk.file <- "Cluster11_GSEA.rnk"
ranks <- read.table(rnk.file, header = TRUE, colClasses = c("character", "numeric"))
PaulineMarangoni commented 5 years ago

Great, it seems that I can move forward now! Thanks again for your speedy reply!

pstew commented 4 years ago

Thanks, had the same issue!