search

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
254 stars 35 forks source link

custom count matrixes #2

Closed Eneritz closed 6 years ago

Eneritz commented 6 years ago

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

constantAmateur commented 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.

Eneritz commented 6 years ago

Thanks Mathew!