Error in colSums(pathway_individualEMs[[i]]) : 'x' must be numeric

saezlab / SLAPenrich

Sample Level Analysis of Pathway Alteration Enrichments

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Error in colSums(pathway_individualEMs[[i]]) : 'x' must be numeric #4

Open gianfilippo opened 5 years ago

gianfilippo commented 5 years ago

Hi,

I get the following error when running the SLAPenrich function: Error in colSums(pathway_individualEMs[[i]]) : 'x' must be numeric

I believe there may be a bug in the main function. It happens when the intersection between a gene set and the tested genes is either empty or a single element.

I modified a couple of lines to fix it. I can send you the modified version of the function, if interested.

Best Gianfilippo

complexgenome commented 3 months ago

@gianfilippo @Nic-Nic I get the same error with pathcom human database:

pathwaycommons_SLAPE_analysis = SLAPE.analyse(EM=df_mutation, PATH_COLLECTION=PATHCOM_HUMAN, GeneLenghts = GECOBLenghts)

Error:

colSums(pathway_individualEMs[[i]]) : 'x' must be numeric

session info: SLAPenrich * 0.1 2024-04-29 [1] Github (saezlab/SLAPenrich@1ea52d3) R version 4.3.2 (2023-10-31)