No rownames for peakmatrix from the ArchR project

venkan commented 11 months ago

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

rcorces commented 11 months ago

Hi @venkan! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

wgao688 commented 3 months ago

Hi @venkan , I have this same issue. Did you find a solution to this?

GreenleafLab / ArchR

No rownames for peakmatrix from the ArchR project #2051