#' 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 = "none", outputfile = "none") {
if(length(mypathways) == 1){
if (mypathways == "") {
stop("Be sure to specify the output of the function getPathwayFromAnalyte() and an output file")
}}
if(length(outputfile) == 1){
if (outputfile == "") {
stop("Be sure to specify the output of the function getPathwayFromAnalyte() and an output file")
}}
if (!all(c(
"pathwayName", "pathwaySource",
"pathwayId", "inputId", "commonName"
) %in% colnames(mypathways))) {
stop("Make sure that your input data is the output of the function getPathwayFromAnalyte()")
}
out <- mypathways[, c(
"pathwayName", "pathwaySource",
"pathwayId", "inputId", "commonName"
)]
utils::write.csv(out, file = outputfile, row.names = F, quote=TRUE)
}
#' Function that writes Fishers Test results, after clustering to a CSV file
#'
#' @param fishResults a data frame returned by function runCombinedFisherTest()
#' @param outputfile name of output file
#' @param rampid whether or not to include rampId (default is FALSE)
#' @export
write_FishersResults <- function(fishResults = "none", outputfile = "none", rampid = FALSE) {
if(length(fishResults) == 1){
if (fishResults == "") {
stop("Be sure to specify the output of the function findCluster()")
}}
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 <- fishResults$cluster_list
out <- fishResults
rampOut <- out$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", "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",
"Cluster", "rampids"
)
rampOut <- rampOut[order(rampOut[, "Holm Adjusted P Value"]), ]
}
# utils::write.csv(rampOut,outputfile,row.names = FALSE)
} else {
rampOut <- "No significant results"
# utils::write.csv(c("No significant results"),outputfile,row.names = FALSE)
}
}
if (!rampid) {
rampOut <- rampOut[, -ncol(rampOut)]
}
if (outputfile=="none") {
return(rampOut[order(rampOut[, "Cluster"]), ])
} else {
utils::write.csv(rampOut[order(rampOut[, "Cluster"]), ], outputfile, row.names = FALSE)
}
}
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