custom count matrixes about soupx

[constantAmateur]

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.

[Eneritz]

Thanks Mathew!