I have a data.frame with 3 columns. The structure of the data.fame is as below
str(data) 'data.frame': 76971772 obs. of 3 variables: $ V1: chr "XH104_AACGAGAGCTAAACTAGCCCTA" "XH104_AACGAGAGCTAAACTAGCCCTA" "XH104_AACGAGAGCTAAACTAGCCCTA" "XH104_AACGAGAGCTAAACTAGCCCTA" ... $ V2: chr "10:100175000-100180000" "10:101065000-101070000" "10:101550000-101555000" "10:101585000-101590000" ... $ V3: int 2 2 2 2 10 1 2 2 2 2 ...
I am trying to convert it into sparseMatrix such that the row name of sparseMatrix is data$V1 and the column name is data$V2. I am using the command given below to do that.
sparse.data <- with(data, sparseMatrix(i=as.numeric(V1), j=as.numeric(V2), x=V3, dimnames=list(levels(V1), levels(V2))))
I keep getting the this error.
Error in sparseMatrix(i = as.numeric(V1), j = as.numeric(V2), x = V3, :
NA's in (i,j) are not allowed
I realized that when I use i=as.numeric(V1) in my command, all the values of V1 become NA.
Can someone suggest how can I solve this error?