#' Function that writes output from getPathwayFromAnalyte() to a CSV file
#'
#' @param mypathways data frame returned by function getPathwayFromAnalyte()
#' @param outputfile name of output file
#' @export
writePathwaysToCSV <- function(mypathways=NULL,outputfile=NULL) {
if(is.null(mypathways) || is.null(outputfile)) {
stop("Be sure to specify the output of the function getPathwayFromAnalyte() and an output file")
}
if(!all(c("pathwayName","pathwaysourceId",
"pathwaysource","commonName") %in% colnames(mypathways))) {
stop("Make sure that your input data is the output of the function getPathwayFromAnalyte()")
}
out= mypathways[,c("pathwayName","pathwaysourceId",
"pathwaysource","commonName")]
utils::write.csv(out,file = outputfile,row.names = F)
}
#' Function that writes Fishers Test results to a CSV file
#'
#' @param fishResults a data frame returned by function runCombinedFisherTest()
#' @param outputfile name of output file
#' @export
write_FishersResults <- function(fishResults=NULL,outputfile=NULL){
if(is.null(fishResults) || is.null(outputfile)) {
stop("Be sure to specify the output of the function findCluster() and an output file")
}
clusters <- fishResults$cluster_list
if(is.null(clusters)) {
out <- fishResults$fishresults
mycols <- setdiff(colnames(out),c("pathwayRampId","pathwayName"))
mycols <- c("pathwayName",mycols)
utils::write.csv(out[,mycols],file=outputfile,row.names=F)
}
else {
cluster_list<-clusters$cluster_list
out <- fishResults
rampOut=out$fishresults
if(!is.null(rampOut)) {
if(out$analyte_type=="both"){
rampOut<-rampOut[,c("pathwayName","Pval.Metab","Num_In_Path.Metab","Total_In_Path.Metab",
"Pval.Gene", "Num_In_Path.Gene","Total_In_Path.Gene", "Pval_combined",
"Pval_combined_FDR","Pval_combined_Holm","pathwaysourceId","pathwaysource",
"cluster_assignment","rampids")]
colnames(rampOut)<-c("Pathway Name", "Raw Fisher's P Value (Metabolites)","User Metabolites in Pathway",
"Total Metabolites in Pathway","Raw Fisher's P Value (Genes)","User Genes in Pathway",
"Total Genes in Pathway","Raw Fisher's P Value (Combined)","FDR Adjusted P Value (Combined)",
"Holm Adjusted P Value (Combined)","Source ID","Source DB","In Cluster","rampids")
rampOut<-rampOut[order(rampOut[,"Holm Adjusted P Value (Combined)"]),]
} else{
results_fisher<-rampOut[,c("pathwayName","Pval","Pval_FDR","Pval_Holm","pathwaysourceId","pathwaysource",
"Num_In_Path","Total_In_Path","cluster_assignment","rampids")]
colnames(rampOut)<-c("Pathway Name", "Raw Fisher's P Value","FDR Adjusted P Value","Holm Adjusted P Value",
"Source ID","Source DB", "User Analytes in Pathway", "Total Analytes in Pathway",
"In Cluster","rampids")
rampOut<-rampOut[order(rampOut[,"Holm Adjusted P Value"]),]
}
utils::write.csv(rampOut,outputfile,row.names = FALSE)
}else{
utils::write.csv(c("No significant results"),outputfile,row.names = FALSE)
}
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.