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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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CreateOmics with class OmicsSurv #78

Open torongs82 opened 5 years ago

torongs82 commented 5 years ago

I runned this code:

data("kirpPheno_df")
data("kirpRNAseq_df")

kidney_Omics <- CreateOmics(
    assayData_df = kirpRNAseq_df,
    pathwayCollection_ls = wikipathways_PC,
    # Exclude the gender indicator for now
    response = kirpPheno_df[, 1:3],
    respType = "surv",
    minPathSize = 5
)

that produced this error:

Creating object of class OmicsSurv ======= Error in validObject(.Object) : invalid class “OmicsSurv” object: 1: invalid object for slot "assayData_df" in class "OmicsSurv": got class "spec_tbl_df", should be or extend class "data.frame" invalid class “OmicsSurv” object: 2: invalid object for slot "assayData_df" in class "OmicsSurv": got class "tbl_df", should be or extend class "data.frame" invalid class “OmicsSurv” object: 3: invalid object for slot "assayData_df" in class "OmicsSurv": got class "tbl", should be or extend class "data.frame" invalid class “OmicsSurv” object: 4: invalid object for slot "assayData_df" in class "OmicsSurv": got class "data.frame", should be or extend class "data.frame"

torongs82 commented 5 years ago

If I runned 

kirpRNAseq_df <- as.data.frame(kirpRNAseq_df)

it worked.