ArchR
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No rownames for peakmatrix from the ArchR project
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