# first i create the new dataframe
data.mean<- data.frame(matrix(nrows=30))

# iterate over every third collumn
for(col in seq(1,length(colnames(data)), by=3)){

    # create a subset from the dataframe and compute the mean of the rows and finally cbind it to the result dataframe
    data.mean <-cbind(data.mean,apply(subset(data, select=seq(col,length.out =   3)),1,mean, na.rm = TRUE))

    # setting the new collumn name to the colname from the old dataset (name of the first replicate)
    colnames(data.mean)[ncol(data.mean)] <- colnames(data)[col]
}