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sqjin / scAI

An unsupervised approach for the integrative analysis of single-cell multi-omics data
GNU General Public License v3.0
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Select highly variable loci for ATAC-seq #11

Open PeterZZQ opened 4 years ago

PeterZZQ commented 4 years ago 
object <- selectFeatures(object, assay = "RNA")
loci.use <- searchGeneRegions(genes = object@var.features[[1]], species = "mouse")
object@var.features[[2]] <- loci.use
object <- run_scAI(object, K, do.fast = TRUE, hvg.use1 = TRUE, hvg.use2 = TRUE)

I cannot run through that code for kidney example, Error shows that

Error in object@norm.data[[2]][object@var.features[[2]], ] : invalid or not-yet-implemented 'Matrix' subsetting

loci seems to be a data frame with 4 columns and the selection requires one region annotation. I think you may miss some function like search_nearby_loci in MATLAB version.

sqjin commented 4 years ago

@PeterZZQ Please check the function findNearbyLoci.