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No rownames for peakmatrix from the ArchR project

Open venkan opened this issue 7 months ago • 2 comments

I have the ArchR project load into proj

getAvailableMatrices(proj)
[1] "GeneScoreMatrix" "PeakMatrix"      "TileMatrix"

To get the peak matrix I used:

peak_matrix <- getMatrixFromProject(proj, "PeakMatrix")

But I see that rownames show NULL:

> peak_matrix
class: RangedSummarizedExperiment
dim: 187739 15031
metadata(0):
assays(1): PeakMatrix
rownames: NULL
rowData names(1): idx
colnames(15031): LRRC15_G3#AGTGCGCTCGTGGAAG-1
  LRRC15_G3#GAAGAGCGTAGAAAGG-1 ... SEAL1_G4#GTGTGATAGACACGGT-1
  SEAL1_G4#GTAGGAGAGGCAAGGG-1
colData names(19): BlacklistRatio DoubletEnrichment ... ReadsInPeaks
  FRIP

I actually wanted the PeakMatrix for creating the Chromatin assay like below:

peak_counts <- readRDS("PeakMatrix.Rds")

chrom_assay <- CreateChromatinAssay(
  counts = peak_counts,
  sep = c("_", "_"),
  min.cells = 100)

But I end up with the error and checked the PeakMatrix and it shows rownames as NULL. Any help please.

Here is the log file:

ArchR-getMatrixFromProject-2974fac9dc44-Date-2023-11-10_Time-15-36-56.log

venkan avatar Nov 10 '23 23:11 venkan