Closed Eneritz closed 6 years ago
Hi Eneritz,
Any count matrix should work, so long as it contains a column for each droplet. The load10X
function is really just a convenience, the key is running:
channel1 = SoupChannel(tod1,toc1,channelName="NameOfChannel1")
channel2 = SoupChannel(tod2,toc2,channelName="NameOfChannel2")
scl = SoupChannelList(list(channel1,channel2))
where tod
is the matrix with all droplets (including the empty ones) and toc
is the sub-matrix that contains only the cell containing droplets. This would be the raw_gene_bc_matrices
and filtered_gene_bc_matrices
respectively when using cellranger output.
load10X
gets these for you from the cellranger output, if you're doing something else you'll have to construct them and input them manually as above.
Thanks Mathew!
Hi Mathew, I just starting using your method and I was wondering if it is possible to upload custom counts matrixes. I am using 10X samples but for some benchmarks instead of using cellranger output I have my own matrixes. Is it possible? Thanks.
Nice work
E