Addition of RcheckLibrary.R file to allow the use of check functions

See project easyRLibrary.git
Commit: 3a360a1d4b4a0f4fc46be3cacf43895b1ce438c2 [3a360a1]
Date: jeudi 22 janvier 2015 16:27:24

RcheckLibrary.R

@@ -0,0 +1,75 @@
+###############################################
+# R check library
+# Coded by : M.Petera, 
+# - -
+# R functions to use in R scripts  
+# (management of various generic subroutines)
+# - -
+# V0 : script structure + first functions
+###############################################
+
+
+# Generic function to return an error if problems have been encountered - - - -
+
+check.err <- function(err.stock){
+
+	# err.stock = vector of results returned by check functions
+
+	if(length(err.stock)!=0){ stop("\n- - - - - - - - -\n",err.stock,"\n- - - - - - - - -\n") }
+
+}
+
+
+
+
+# Table match check functions - - - - - - - - - - - - - - - - - - - - - - - - -
+
+# To check if dataMatrix and (variable or sample)Metadata match regarding identifiers
+match2 <- function(dataMatrix, Metadata, Mtype){
+
+	# dataMatrix = data.frame containing dataMatrix
+	# Metadata = data.frame containing sampleMetadata or variableMetadata
+	# Mtype = "sample" or "variable" depending on Metadata content
+
+	err.stock <- NULL # error vector
+
+	id2 <- Metadata[,1]
+	if(Mtype=="sample"){ id1 <- colnames(dataMatrix)[-1] }
+	if(Mtype=="variable"){ id1 <- dataMatrix[,1] }
+
+	if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
+		err.stock <- c("\nData matrix and ",Mtype," metadata do not match regarding ",Mtype," identifiers.\n",
+					"Please check your data.\n")
+	}
+
+	return(err.stock)
+
+}
+
+# To check if the 3 standard tables match regarding identifiers
+match3 <- function(dataMatrix, sampleMetadata, variableMetadata){
+
+	# dataMatrix = data.frame containing dataMatrix
+	# sampleMetadata = data.frame containing sampleMetadata
+	# variableMetadata = data.frame containing variableMetadata
+
+	err.stock <- NULL # error vector
+
+	id1 <- colnames(dataMatrix)[-1]
+	id2 <- sampleMetadata[,1]
+	id3 <- dataMatrix[,1]
+	id4 <- variableMetadata[,1]
+
+	if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
+		err.stock <- c(err.stock,"\nData matrix and sample metadata do not match regarding sample identifiers.")
+	}
+
+	if( length(which(id3%in%id4))!=length(id3) || length(which(id4%in%id3))!=length(id4) ){
+		err.stock <- c(err.stock,"\nData matrix and variable metadata do not match regarding variable identifiers.")
+	}
+
+	if(length(err.stock)!=0){ err.stock <- c(err.stock,"\nPlease check your data.\n") }
+
+	return(err.stock)
+
+}