#' @importFrom data.table fread
#' @export
import_openswath <- function(input_search_results) {
message("Message: It starts reading raw OpenSWATH search results...")
raw <- fread(input=input_search_results, head=T)
names(raw)[1] <- "PeptideIon"
raw$PeptideIon <- paste(sapply(strsplit(raw$PeptideIon, "_"), "[[", 2), "_", sapply(strsplit(raw$PeptideIon, "_"), "[[", 3), sep="")
data <- raw[-which(grepl("DECOY", raw$ProteinName)), ]
summarize_data(data)
#data$filename <- sapply(strsplit(data$filename, "/"), "[[", 4)
return(data)
}
#' @export
read_sample_annotation <- function(input_file) {
anno <- data.frame(read.table(file = input_file, sep = "\t", head = T, stringsAsFactors = F))
if (!"sample_id" %in% names(anno) || !"filename" %in% names(anno)) {
STOP("Please choose a valid sample annotation table that contains at least sample_id and filename columns.")
}
return(anno)
}
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