questions in the first createArrowFiles

[1221li]

In my fragment file, there are more than 300,000 barcodes after removing the duplicates. However, I imported the fragment file into archR and created the arrow file. Without adding any filtering conditions, there are only more than two thousand cells. I do not understand this, and I hope you can provide me with any suggestions about how do I get all barcodes in the Arrow file

ArrowFiles <- createArrowFiles(inputFiles = inputFiles,sampleNames = names(inputFiles),filterTSS = NULL,filterFrags = NULL,addTileMat = TRUE,addGeneScoreMat = TRUE,geneAnnotation = geneAnnotation,genomeAnnotation = genomeAnnotation)

[rcorces]

filterFrags and filterTSS are deprecated. You need to use minFrags and minTSS. This is somewhat reflected in the function documentation as filterFrags and filterTSS are no longer defined.
https://www.archrproject.com/reference/createArrowFiles.html

ArchR/R/CreateArrow.R

Line 107 in 968e442

if(!is.null(filterFrags)){

[1221li]

Thank you for your reply. I have another question about "Pairwise Testing Between Groups".
markerTest <- getMarkerFeatures(
ArchRProj = projHeme5,
useMatrix = "PeakMatrix",
groupBy = "Clusters2",
testMethod = "wilcoxon",
bias = c("TSSEnrichment", "log10(nFrags)"),
useGroups = "Erythroid",
bgdGroups = "Progenitor"
)
I can get the genelist in useGroup with this code, but I don't know how to get the gebelist in bgdGroup 。What should I do if I want to get gene list from bgdgroup。
I look forward to your reply！

[rcorces]

Its beneficial to not ask two questions in the same thread because this makes it harder for others to find previous questions.

To answer your question, I think there is some confusion on useGroups and bgdGroups. These are groups of cells, not groups of genes.