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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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how to produce a coverage corrected matrix #14

Closed JLiLab closed 4 years ago

JLiLab commented 4 years ago

Thank you for sharing the pipeline!

I wonder if we can create a coverage corrected matrix and export it for other methods. The batch.aligned.data slot is empty after running combined coverage correction alignment.

Thank you,

James

rezakj commented 4 years ago

Hi James,

Yes possible,

run this:

my.obj <- run.pca(my.obj, method = "gene.model", gene.list = my.obj@gene.model,data.type = "main")

my.obj <- run.impute(my.obj, dims = 1:10, nn = 10, data.type = "pca")

And your data will be at my.obj@imputed.data

Reza

JLiLab commented 4 years ago

Thank you!