Hello,
Great package. I am running Signac on my data, and am running into an issue at the TSSEnrichment step. When running the function, I get the following error:
Error in SetAssayData.ChromatinAssay(object = object[[assay]], slot = slot, :
Position enrichment must be provided as a matrix or sparseMatrix
I am able to follow the Vignette fine, so it's something with my data. Here is my code:
counts <- Read10X_h5(filename = "/Users/seandelao/Desktop/Signac/12wpc_epcam/filtered_peak_bc_matrix.h5")
metadata <- read.csv(file = "/Users/seandelao/Desktop/Signac/12wpc_epcam/singlecell.csv",
header = TRUE,
row.names = 1
)
chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
genome = 'hg38',
fragments = "/Users/seandelao/Desktop/Signac/12wpc_epcam/fragments.tsv.gz",
min.cells = 10,
min.features = 200
)
pbmc <- CreateSeuratObject(
counts = chrom_assay,
assay = "peaks",
meta.data = metadata
)
pbmc
pbmc[['peaks']]
granges(pbmc)
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"
Annotation(pbmc) <- annotations
pbmc <- NucleosomeSignal(object = pbmc)
pbmc
pbmc <- TSSEnrichment(object = pbmc, fast = FALSE)
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