qcAndArchR.yml

## *** QC-FILTERING PARAMS ***: 
# Minimum number of unique reads passing cells must have 
minUniqueReads: 100
# Proportion of  of total reads expected to be background. (Between 0 and 1) 
backgroundRatio: 0.03
# Top Percent of Cells which will be used to calculate QC metric thresholds (from 0-100)
topPercentCells: 10

## *** ARCHR ANALYSIS PARAMS ***: 
## .ARROW CREATION PARAMS 
# Minimum TSS enrichment score (as defined by ArchR) passing cells must have 
minimumTSS:  1
# Minimum Fragments 
minimumFragments: 0

## DIMENSIONALITY REDUCTION PARAMS 
#  Number of iterations of LSI to be run during dimensionality reduction (on TileMatrix)
LSI_Iterations: 2

## CLUSTERING PARAMS 
# Maximum number of clusters to group cells into 
maxClusters: 2

# Number of neighboring sample points used for UMAP. 
# Larger values result in more global views while smaller values result in more local data 
# being preserved from (2-100)
nNeighbors: 50

# Specifying whether to run certain aspects of automated analysis
# Generate UMAP from dimensionality reduction output? 
plotUMAP: true

# Calculate marker genes from ArchR extrapolated genescores per cluster?
getMarkerGenes: false