Entering edit mode
18 months ago
Chihiro
•
0
Hi!
I'm currently using ArchR for a scATAC-seq analysis. I'd like to get BAM files after batch correction using "Harmony" in ArchR. Namely, a bam file for each cluster in each sample.
I would appreciate any help.
# after reading inputFiles (2 inputFiles from 2 samples)
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = names(inputFiles),
minTSS = 6,
minFrags = 2000,
maxFrags = 1e+05,
addTileMat = TRUE,
addGeneScoreMat = TRUE, force=T
)
doubScores <- addDoubletScores(
input = ArrowFiles,
k = 10,
knnMethod = "UMAP",
LSIMethod = 1
)
proj <- ArchRProject(
ArrowFiles = ArrowFiles,
outputDirectory = "HemeTutorial",
copyArrows = TRUE
)
getAvailableMatrices(proj)
proj <- filterDoublets(ArchRProj = proj, filterRatio = 2.5)
proj <- addIterativeLSI(ArchRProj = proj, useMatrix = "TileMatrix", name = "IterativeLSI")
proj <- addHarmony(
ArchRProj = proj,
reducedDims = "IterativeLSI",
name = "Harmony",
groupBy = "Sample"
)
proj <- addClusters(input = proj, reducedDims = "Harmony")