6a. Add imputed weights

proj3 <- addImputeWeights(proj2)

6b. Add reproducible, consensus peak set

Drop ribosomal genes from downstream analysis.

no_ribo_genes <- getGenes(proj3)
no_ribo_genes <- no_ribo_genes[!grepl("^Rp[sl][[:digit:]]|^Rplp[[:digit:]]|^Rpsa", no_ribo_genes$symbol)]
proj3 <- addGeneScoreMatrix(
    input = proj3, 
    genes = no_ribo_genes,
    matrixName = "GeneScoreMatrix_no_ribosomal",
    threads=1,
    force=TRUE)
proj3 <- addGroupCoverages(proj3,
                           groupBy="Clusters_LSI",
                           minCells = 5,
                           maxReplicates = 10,
                           maxFragments = 100 * 10^6,
                           threads=1)
proj3 <- addReproduciblePeakSet(proj3,
                                groupBy="Clusters_LSI")
proj3 <- addPeakMatrix(proj3)

6c. Identify co-accessible peaks

proj3 <- addCoAccessibility(
    ArchRProj = proj3,
    reducedDims = "LSI_Harmony"
)

cA <- getCoAccessibility(
    ArchRProj = proj3,
    corCutOff = 0.5,
    resolution = 1,
    returnLoops = FALSE
)

proj3 <- saveArchRProject(ArchRProj = proj3)
save.image(paste0(sample_name, "_project3_", Sys.Date(), ".RData"))