#' Gene set enrichment analysis
#
#' @param geneSet A list of gene symbols.
#' @param featureMapping A list of data frames containing 'Data.Names', 'Gene.Symbols', 'Display.Names' for each of the data blocks.
genesetEnrichment <- function(geneSet, featureMapping) {
# Get dataset
library(sear)
candidates <- geneSet
if (!is.null(featureMapping)){
for (name in candidates){
warning(sprintf("%s", name))
}
}
# Perform 'sear'
result <- sear::sear(candidates)
result <- dplyr::arrange(result, fdr)
result <- result[1:20, c("collection", "geneset", "fdr")]
result[, -c(1,2)] <- signif(result[, -c(1,2)], digits = 3)
result
}
#' Match with existing Protein-Protein Interaction data
#
#' If there is a match, returns the index of the match in the PPI data in a vector of length 'edges'
#' 'edges' and 'data' both two column data frames
#
#' @param edges A data frame consisting of two proteins that have an edge.
#' @param data A data frame consisting of two columns of proteins that interact
matchPPI <- function(edges, data){
matches <- prodlim::row.match(edges, data)
}
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