R/checkData.R

In bvnlab/SCATTome: FluidgmR

checkData <-
function(d, Type=c("Train","Test")){

DataStatus=is.data.frame(d);
if(DataStatus==FALSE){
print("Data is not a data frame. Kindly check data format");
return(0)
}

ID<-d[,1];
ID.Status=is.character(na.omit(ID));
if(ID.Status==FALSE){
print("Cell ID not valid character. Check cell ID format");
return(0)
}else{
n1<-length(ID)-length(na.omit(ID))
if(n1>0){
print("Cell ID Missing. Missing cell ID not allowed.");
return(0);
}
n2<-length(ID)-length(unique(ID));
if(n2>0){
print("Repetitive cell ID not allowed");
return(0);
}
}

if(Type=="Train"){
Status=d[,dim(d)[2]];
Status=na.omit(unique(Status));
ClassCat=length(Status);
l1<-which(Status==1);
l2<-which(Status==0);

if(!(ClassCat==2)){
print("Two classes are required. Data does not have two classes.");
return(0);
}

if((length(l1)==0) || (length(l2)==0)){
print("Class labels need to be 0 and 1. Please check data");
return(0);
}
}

if(Type=="Train"){
Gene<-d[,2:(dim(d)[2]-1)];
}else{
Gene<-d[,2:(dim(d)[2])];
}
n3<-length(colnames(Gene))-length(unique(colnames(Gene)));
if(n3>0){
print("Repetitive variable names not allowed");
return(0);
}

for(i in 1:dim(Gene)[2]){
DataType<-is.numeric(na.omit(Gene[,i]));
DataLength=length(na.omit(Gene[,i]));
if(DataLength>0){
if(DataType==FALSE){
print("Non-numeric data in gene expression");
print(paste("Check the following gene: ", colnames(Gene)[i], sep=""));
return(0);
}
}else{
print(paste("Warning: ", colnames(Gene)[i], " contains all NAs.", sep="")); 
}
}
print("Cell ID check OK");
print("Class Status check OK");
print("Gene expression data type check OK");
return(1);

}