#' Define files
#'
#' This function defines environmental files.
#' @export
#' @param FILE name of *.bcmatrix.xlsx in current working directory
#' @examples
#' defineFiles("/path/to/bcmatric.xlsx")
defineFiles <- function(FILE=FILE) {
#FILE=grep("*.bcmatrix.xlsx", list.files(), value=T)
#ifelse(length(FILE)==1, paste("Found datafile:", FILE), q("no", status=1))
assign("WDIR", getwd(), .GlobalEnv)
DF=gdata::read.xls(paste(WDIR, FILE, sep="/"), sheet = 1, header = TRUE, stringsAsFactors=F)
SUMMARY=gsub("bcmatrix", "bc_summary", FILE)
#ifelse(length(grep(SUMMARY, list.files(), value=T))==1, paste("Found metafile:", SUMMARY), q("no", status=1))
META=gdata::read.xls(paste(WDIR, SUMMARY, sep="/"), sheet = 1, header = TRUE, stringsAsFactors=F)
#rownames(REFVALUES)=REFVALUES$Sample
AMPLICONS=as.character(DF$Target)
row.names(DF)=AMPLICONS
DF=DF[,-1:-2]
SAMPLES=as.vector(META$Sample.Name)
colnames(DF)=SAMPLES
assign("LEN", length(SAMPLES)+1, .GlobalEnv)
#NORM=META$Mapped.Reads
#assign("REFVALUES", REFVALUES, .GlobalEnv)
assign("FILE", FILE, .GlobalEnv)
assign("SUMMARY", SUMMARY, .GlobalEnv)
assign("DF", DF, .GlobalEnv)
assign("SAMPLES", SAMPLES, .GlobalEnv)
assign("META", META, .GlobalEnv)
}
#' Define variables
#'
#' This function defines environmental variables.
#' @export
#' @examples
#' defineVariables()
defineVariables <- function() {
assign("TIME", format(Sys.time(), "%H:%M:%S"), .GlobalEnv)
assign("DATE", format(Sys.time(), "%Y-%m-%d"), .GlobalEnv)
assign("PROJECTID", paste(DATE, gsub(":", "", TIME), sep="-"), .GlobalEnv)
dir.create(paste(PROJECTID, "data", sep="/"), showWarnings = FALSE, recursive = TRUE)
dir.create(paste(PROJECTID, "figures", sep="/"), showWarnings = FALSE, recursive = TRUE)
}
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