RunCCA() crash
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8 weeks ago
Beth • 0

Hi, i want to RunCCA with my datasets for scRNA and scATAC assays (see test files attached here: https://drive.google.com/drive/folders/1C8zgkC_uNOPOc32dFKw6u6QF1n0UDB6R?usp=share_link). After running a function R session just crashes, how I can solve this problem?

Script for generating files (input for the script - SeuratObject for RNA and peaks assay (adrenal_EC in archive), fragment objects (listed as "sample 1 adrenal", "sample 16 adrenal", "sample 27 adrenal", "sample 31 adrenal" here: https://descartes.brotmanbaty.org/bbi/human-chromatin-during-development/), fragment index files (attached in archive).

Script:

library(Seurat)
library(Signac)
library(EnsDb.Hsapiens.v86)
adrenal_EC <- subset(adrenal_EC, subset = nFeature_RNA > 200 & nFeature_RNA < 12500)
frags1 <- CreateFragmentObject(path = "/fast/AG_Bunina/Lisa/R/sample_1_adrenal.fragments.txt.gz")
frags16 <- CreateFragmentObject(path = "/fast/AG_Bunina/Lisa/R/sample_16_adrenal.fragments.txt.gz")
frags27 <- CreateFragmentObject(path = "/fast/AG_Bunina/Lisa/R/sample_27_adrenal.fragments.txt.gz")
frags31 <- CreateFragmentObject(path = "/fast/AG_Bunina/Lisa/R/sample_27_adrenal.fragments.txt.gz")
fragpath = dir('/fast/AG_Bunina/Lisa/R/',"*gz$",full.names=TRUE)
peaks<-GetAssayData(object = adrenal_EC, assay = "peaks", slot = "counts")
assay_test <- CreateChromatinAssay(counts = peaks,fragments = list(frags1, frags16, frags27, frags31))

pbmc.rna <-CreateSeuratObject(adrenal_EC@assays[[1]])
pbmc.rna <- NormalizeData(pbmc.rna)
pbmc.rna <- FindVariableFeatures(pbmc.rna)
pbmc.rna <- ScaleData(pbmc.rna)
pbmc.rna <- RunPCA(pbmc.rna)
pbmc.rna <- RunUMAP(pbmc.rna, dims = 1:30)

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevelsStyle(annotations) <- "UCSC"
genome(annotations) <- "hg38"
Annotation(assay_test) <- annotations
pbmc.atac <-CreateSeuratObject(assay_test, assay = "ATAC")
pbmc.atac <- RunTFIDF(pbmc.atac)
pbmc.atac <- FindTopFeatures(pbmc.atac, min.cutoff = "q0")
pbmc.atac <- NormalizeData(pbmc.atac)
pbmc.atac <- ScaleData(pbmc.atac, features = rownames(pbmc.atac))

testRNA <- subset(pbmc.rna, cells = colnames(pbmc.rna)[1:30])
testATAC <- subset(pbmc.atac, cells = colnames(pbmc.atac)[1:30])

saveRDS(testRNA, "testRNA.rds")
saveRDS(testATAC, "testATAC.rds")

cca<-RunCCA(testATAC, testRNA)
integration scATAC Seurat RunCCA scRNA • 198 views
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how much memory do you have available?

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