I had 6 treatment and 6 control samples which were sequences on Illumina. I used the cell ranger --count function to sequence all of my samples together since they were sequenced on the same platform. It gave me a bunch of outputs from which I used a raw.h5 file to generate a Seurat object which didn't work. I used the Read10x_h5 function from Seurat in R which did read the file however when I used the CreateSeuratObject function to make suerat object it gives me the following error
"$ operator not defined for this S4 class"
so I used str function to take a look at the class. and the only thing I was able to see was as follow
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots ..@ i : int [1:298187053] 9 17 30 32 34 40 50 63 68 69 ... ..@ p : int [1:167638] 0 3243 4474 4998 5732 7323 8429 11210 12961 17019 ... ..@ Dim : int [1:2] 32285 167637 ..@ Dimnames:List of 2 .. ..$ : chr [1:32285] "Xkr4" "Gm1992" "Gm19938" "Gm37381" ... .. ..$ : chr [1:167637] "AAACCCAAGAAGGATG-1" "AAACCCAAGACCAAAT-1" "AAACCCAAGACCAACG-1" "AAACCCAAGACCATTC-1" ... ..@ x : num [1:298187053] 1 1 1 4 1 2 1 11 1 2 ... ..@ factors : list()
