Add Module Scores to an ArchRProject — addModuleScore • ArchR

This function calculates a module score from a set of features across all cells. This allows for grouping of multiple features together into a single quantitative measurement. Currently, this function only works for modules derived from the GeneScoreMatrix. Each module is added as a new column in cellColData

addModuleScore(
  ArchRProj = NULL,
  useMatrix = NULL,
  name = "Module",
  features = NULL,
  nBin = 25,
  nBgd = 100,
  seed = 1,
  threads = getArchRThreads(),
  verbose = TRUE,
  logFile = createLogFile("addModuleScore")
)

Arguments

ArchRProj: An ArchRProject object.
useMatrix: The name of the matrix to be used for calculation of the module score. See getAvailableMatrices() to view available options.
name: The name to be given to the designated module. If features is a list, this name will be prepended to the feature set names given in the list as shown below.
features: A list of feature names to be grouped into modules. For example, list(BScore = c("MS4A1", "CD79A", "CD74"), TScore = c("CD3D", "CD8A", "GZMB", "CCR7", "LEF1")). Each named element in this list will be stored as a separate module. The examples given in these parameters would yield two modules called Module.Bscore and Module.Tscore. If the elements of this list are not named, they will be numbered in order, i.e. Module1, Module2.
nBin: The number of bins to use to divide all features for identification of signal-matched features for background calculation
nBgd: The number of background features to use for signal normalization.
seed: A number to be used as the seed for random number generation required when sampling cells for the background set. It is recommended to keep track of the seed used so that you can reproduce results downstream.
threads: The number of threads to be used for parallel computing.
verbose: A boolean value that determines whether standard output includes verbose sections.
logFile: The path to a file to be used for logging ArchR output.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Add Module Score
proj <- addModuleScore(proj, useMatrix = "GeneScoreMatrix", nBin = 25, nBgd = 25, features = list(TScore = c('CD3D', 'CD3E')))

#Check
split(proj@cellColData$Module.TScore, proj@cellColData$CellType) %>% lapply(mean) %>% unlist
#        B         M         T 
# -4.352769 -8.438259  9.942678 

#Get T cell Features
features <- getGenes()
T <- features[features$symbol %in% c("CD3D", "CD3E")]
B <- features[features$symbol %in% c("MS4A1")]

# Add Module Score
proj <- addModuleScore(proj, useMatrix = "TileMatrix", nBin = 25, nBgd = 25, features = list(TScore = T, BScore = B))

#Check
split(proj@cellColData$Module.TScore, proj@cellColData$CellType) %>% lapply(mean) %>% unlist
#          B           M           T 
# -0.03866667 -0.05303030  0.10306122

split(proj@cellColData$Module.BScore, proj@cellColData$CellType) %>% lapply(mean) %>% unlist
#          B           M           T 
# 0.10000000 -0.03939394 -0.05387755