elelab / campp2 Goto Github PK

library(SummarizedExperiment)

create_summarized_experiment <- function(gene_counts, sample_metadata) {
  # Check if input data frames have the same number of samples
  if (ncol(gene_counts) != nrow(sample_metadata)) {
    stop("The number of columns in gene_counts must match the number of rows in sample_metadata.")
  }
  
  # Check if row names in sample_metadata match column names in gene_counts
  if (!all(rownames(sample_metadata) %in% colnames(gene_counts))) {
    stop("All row names in sample_metadata must be present in the column names of gene_counts.")
  }
  
  # Create the SummarizedExperiment object
  se <- SummarizedExperiment(assays = list(counts = gene_counts),
                             colData = sample_metadata)
  
  return(se)
}

git clone --mirror <repository_url>
cd <repository_name>.git
git filter-branch --index-filter "git rm -rf --cached --ignore-unmatch <path_to_large_file>" --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all
git gc --prune=now --aggressive
git push --force

--- re-building ‘vignette_campp2.Rmd’ using rmarkdown
Quitting from lines 261-262 (vignette_campp2.Rmd) 
Error: processing vignette 'vignette_campp2.Rmd' failed with diagnostics:
package or namespace load failed for 'CAMPP2':
 object 'predict' is not exported by 'namespace:randomForest'
--- failed re-building ‘vignette_campp2.Rmd’