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opain / TWAS-GSEA

R script that performs gene-set or gene property analysis using TWAS results.
GNU General Public License v3.0
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Can not find example file: --gmt_file #1

Closed LDHHAHA closed 2 years ago

LDHHAHA commented 3 years ago

Hi @opain ,i had completed the Predicting TWAS features (FeaturePred). When i run the GSEA example data, i could not find your gmt_file. So i download the gmt file from msigdb(http://www.gsea-msigdb.org/gsea/downloads.jsp),msigdb.v7.4.entrez.gmt. but it did not work. the code and the error: Rscript TWAS-GSEA.V1.0.R \

--twas_results ukbiobank-2017-1160-prePRS-fusion.tsv.GW \ --pos CMC.BRAIN.RNASEQ.pos \ --gmt_file ./GSEA.input/msigdb.v7.4.entrez.gmt \ --expression_ref CMC.BRAIN.RNASEQ_GeneX_all_MINI.csv \ --output demo Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : long flag "pos" is invalid Calls: parse_args -> parse_options -> getopt_options Execution halted.

look forward for your help. Thanks.

opain commented 3 years ago

Hello @LDHHAHA,

Apologies, I believe this is due to changes in TWAS-GSEA. Please use the latest version, TWAS-GSEA.V1.2.R. I was not very familiar with git when I set this repo up, hence having multiple versions in a github repo. I have now removed the old versions of TWAS-GSEA, and changed the example code to use V1.2.

.gmt files from msigdb are the correct format.

Let me know if you still get the same error.

Best wishes,

Ollie