Question

system.file() failed to load .gmt file.

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Mikołaj Mierzejewski • 0

@d312723d

Last seen 23 months ago

Poland

Hello everyone Im trying to load .gmt file into my project. Unfortunately function system.file() can't find my file. Pathway file has been downloaded from MSigDB - curated gene sets. R version - 4.2.1 Rstudio version - 2022.07.1 Build 554 pathwayPCA version - 1.12.0

I tried adding path to sytem.file() and still no success.

gmt_path <- system.file('extdata', 'c2.all.v2022.1.Hs.entrez.gmt', package = "pathwayPCA" ,mustWork = TRUE)

pathwayPCA Gsea • 1.2k views

ADD COMMENT • link updated 2.1 years ago by gabriel.odom • 0 • written 2.1 years ago by Mikołaj Mierzejewski • 0

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Hi Mikolaj, I'm the maintainer for pathwayPCA. If you run into bugs, please report them here: https://github.com/gabrielodom/pathwayPCA/issues

ADD REPLY • link 2.1 years ago gabriel.odom • 0

score 2 · Accepted Answer · 2022-11-01

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 13 minutes ago

United States

Did you actually download the .gmt file into the extdata subdirectory of the pathwayPCA library directory? If so, don't do that. The library directory structure is meant to contain code and data for the package, not files that the end user has downloaded.

More likely you have downloaded the file to your working directory, which is what you should have done, and to load the file you don't need system.file. Instead you can just point to the file name without the path, because R will look in your working directory for files.