NGS-Data-Filter

data-filter

filter <- function(threshold,zeros,countData){
        #1,threshold is the critical mean value of each row;
        #2,countdata is the input original countdata that is going to filter;
        #3,zeros is the critical number of zero reads that each row contained that would filtered out,
        #every row that contain more than this number of zero reads will be deleted. 
        Means <- rowMeans(countData, na.rm = FALSE)
        fullcountdata <- cbind(countData,Means)
        filcountdata <- subset(fullcountdata,Means>threshold)
        filcountdata$Means <- NULL
        #delete the rows that have zero reads less than "zeros" number.
        filcountdata<-filcountdata[rowSums(filcountdata==0)<=zeros,]
        #save the filtered data into the csv file called filcountdata.csv
        write.csv(filcountdata,file="filcountdata.csv")
        filcountdata
        
}