diff --git a/NAMESPACE b/NAMESPACE
index 777fa855..1a99c305 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(agrestiCoullCI)
+export(arrayCompartments)
 export(bootstrapCompartments)
 export(condenseRE)
 export(condenseSE)
@@ -13,8 +14,6 @@ export(fisherZ)
 export(fixCompartments)
 export(flogit)
 export(getABSignal)
-export(getATACABsignal)
-export(getArrayABsignal)
 export(getAssayNames)
 export(getBinMatrix)
 export(getChrs)
diff --git a/R/arrayCompartments.R b/R/arrayCompartments.R
new file mode 100644
index 00000000..4bff477c
--- /dev/null
+++ b/R/arrayCompartments.R
@@ -0,0 +1,97 @@
+#' @title Estimate A/B compartments from methylation array data
+#'
+#' @description
+#' \code{arrayCompartments} returns estimated A/B compartments from methylation array data.
+#'
+#' @param obj Input SummarizedExperiment object
+#' @param res Compartment resolution in bp
+#' @param chr What chromosome to work on (leave as NULL to run on all chromosomes)
+#' @param targets Samples/cells to shrink towards
+#' @param preprocess Whether to preprocess the arrays prior to compartment inference
+#' @param parallel Whether to run samples in parallel
+#' @param cores How many cores to use when running samples in parallel
+#' @param bootstrap Whether we should perform bootstrapping of inferred compartments
+#' @param num.bootstraps How many bootstraps to run
+#' @param boot.parallel Whether to run the bootstrapping in parallel
+#' @param boot.cores How many cores to use for the bootstrapping
+#' @param genome What genome to work on ("hg19", "hg38", "mm9", "mm10")
+#' @param other Another arbitrary genome to compute compartments on
+#' @param group Whether to treat this as a group set of samples
+#' @param array.type What type of array is this ("hm450", "EPIC")
+#'
+#' @return A RaggedExperiment of inferred compartments
+#' @import SummarizedExperiment
+#' @import RaggedExperiment
+#' @importFrom parallel mclapply
+#' @importFrom GenomeInfoDb keepSeqlevels
+#' @importFrom methods as
+#' @export
+#'
+#' @examples
+#'
+#' if (requireNamespace("minfi", quietly = TRUE)) {
+#'   data("array_data_chr14", package = "compartmap")
+#'   array_compartments <- arrayCompartments(
+#'     array.data.chr14,
+#'     chr="chr14",
+#'     parallel=FALSE,
+#'     bootstrap=FALSE,
+#'     genome="hg19",
+#'     array.type="hm450"
+#'   )
+#' }
+arrayCompartments <- function(
+  obj,
+  res = 1e6,
+  chr = NULL,
+  targets = NULL,
+  preprocess = TRUE,
+  parallel = TRUE,
+  cores = 2,
+  bootstrap = TRUE,
+  num.bootstraps = 1000,
+  boot.parallel = TRUE,
+  boot.cores = 2,
+  genome = c("hg19", "hg38", "mm9", "mm10"),
+  group = FALSE,
+  other = NULL,
+  array.type = c("hm450", "EPIC")
+) {
+  verifySE(obj)
+  verifyCoords(obj)
+  verifyAssayNames(obj, assay = "array")
+
+  # preprocess the arrays
+  if (preprocess) {
+    obj <- preprocessArrays(
+      obj = obj,
+      genome = genome,
+      other = other,
+      array.type = array.type
+    )
+  }
+
+  # critical check if imputation was _not_ done
+  # to send things back to beta land
+  is.beta <- min(assays(obj)$Beta, na.rm = TRUE) > 0
+  if (!is.beta) {
+    # send things back to beta land
+    assays(obj)$Beta <- fexpit(assays(obj)$Beta)
+  }
+
+  getCompartments(
+    obj = obj,
+    assay = "array",
+    res = res,
+    parallel = parallel,
+    chr = chr,
+    targets = targets,
+    cores = cores,
+    bootstrap = bootstrap,
+    num.bootstraps = num.bootstraps,
+    boot.parallel = boot.parallel,
+    boot.cores = boot.cores,
+    genome = genome,
+    group = group
+  )
+}
diff --git a/R/getArrayABsignal.R b/R/getArrayABsignal.R
deleted file mode 100644
index a3eb8670..00000000
--- a/R/getArrayABsignal.R
+++ /dev/null
@@ -1,298 +0,0 @@
-#' @title Estimate A/B compartments from methylation array data
-#'
-#' @description
-#' \code{getArrayABsignal} returns estimated A/B compartments from methylation array data.
-#'
-#' @param obj Input SummarizedExperiment object
-#' @param res Compartment resolution in bp
-#' @param parallel Whether to run samples in parallel
-#' @param chr What chromosome to work on (leave as NULL to run on all chromosomes)
-#' @param targets Samples/cells to shrink towards
-#' @param preprocess Whether to preprocess the arrays prior to compartment inference
-#' @param cores How many cores to use when running samples in parallel
-#' @param bootstrap Whether we should perform bootstrapping of inferred compartments
-#' @param num.bootstraps How many bootstraps to run
-#' @param genome What genome to work on ("hg19", "hg38", "mm9", "mm10")
-#' @param other Another arbitrary genome to compute compartments on
-#' @param array.type What type of array is this ("hm450", "EPIC")
-#' @param group Whether to treat this as a group set of samples
-#' @param boot.parallel Whether to run the bootstrapping in parallel
-#' @param boot.cores How many cores to use for the bootstrapping
-#'
-#' @return A RaggedExperiment of inferred compartments
-#' @import SummarizedExperiment
-#' @import RaggedExperiment
-#' @importFrom parallel mclapply
-#' @importFrom GenomeInfoDb keepSeqlevels
-#' @importFrom methods as
-#' @export
-#'
-#' @examples
-#'
-#' if (requireNamespace("minfi", quietly = TRUE)) {
-#'   data("array_data_chr14", package = "compartmap")
-#'   array_compartments <- getArrayABsignal(
-#'     array.data.chr14,
-#'     parallel=FALSE,
-#'     chr="chr14",
-#'     bootstrap=FALSE,
-#'     genome="hg19",
-#'     array.type="hm450"
-#'   )
-#' }
-getArrayABsignal <- function(
-  obj,
-  res = 1e6,
-  parallel = TRUE,
-  chr = NULL,
-  targets = NULL,
-  preprocess = TRUE,
-  cores = 2,
-  bootstrap = TRUE,
-  num.bootstraps = 1000,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  array.type = c("hm450", "EPIC"),
-  group = FALSE,
-  boot.parallel = TRUE,
-  boot.cores = 2
-) {
-  verifySE(obj)
-  verifyCoords(obj)
-  verifyAssayNames(obj, assay = "array")
-
-  # preprocess the arrays
-  if (preprocess) {
-    obj <- preprocessArrays(
-      obj = obj,
-      genome = genome,
-      other = other,
-      array.type = array.type
-    )
-  }
-
-  # critical check if imputation was _not_ done
-  # to send things back to beta land
-  is.beta <- min(assays(obj)$Beta, na.rm = TRUE) > 0
-  if (!is.beta) {
-    # send things back to beta land
-    assays(obj)$Beta <- fexpit(assays(obj)$Beta)
-  }
-
-  # gather the chromosomes we are working on
-  if (is.null(chr)) {
-    message("Assuming we want to process all chromosomes.")
-    # get what chromosomes we want
-    chr <- getChrs(obj)
-  }
-
-  # get the column names
-  if (is.null(colnames(obj))) stop("colnames needs to be sample names.")
-  columns <- colnames(obj)
-  names(columns) <- columns
-
-  # precompute global means
-  prior.means <- getGlobalMeans(obj = obj, targets = targets, assay = "array")
-
-  if (bootstrap) {
-    message("Pre-computing the bootstrap global means.")
-    bmeans <- precomputeBootstrapMeans(
-      obj = obj,
-      targets = targets,
-      num.bootstraps = num.bootstraps,
-      assay = "array",
-      parallel = parallel,
-      num.cores = cores
-    )
-  }
-
-  if (group) {
-    array.compartments.list <- mclapply(chr, function(c) {
-      .arrayCompartments(
-        obj, obj,
-        res = res,
-        chr = c,
-        targets = targets,
-        genome = genome,
-        bootstrap = bootstrap,
-        num.bootstraps = num.bootstraps,
-        prior.means = prior.means,
-        parallel = boot.parallel,
-        cores = boot.cores,
-        group = group,
-        bootstrap.means = bmeans
-      )
-    }, mc.cores = cores)
-    array.compartments <- sort(unlist(as(array.compartments.list, "GRangesList")))
-    return(array.compartments)
-  }
-
-  array.compartments <- mclapply(columns, function(s) {
-    obj.sub <- obj[, s]
-    message("Working on ", s)
-    array.compartments.list <- lapply(chr, function(c) {
-      .arrayCompartments(
-        obj.sub, obj,
-        res = res,
-        chr = c,
-        targets = targets,
-        genome = genome,
-        bootstrap = bootstrap,
-        prior.means = prior.means,
-        num.bootstraps = num.bootstraps,
-        parallel = boot.parallel,
-        cores = boot.cores,
-        group = group,
-        bootstrap.means = bmeans
-      )
-    })
-    sort(unlist(as(array.compartments.list, "GRangesList")))
-  }, mc.cores = ifelse(parallel, cores, 1), mc.preschedule = F)
-
-  array.compartments <- as(array.compartments, "CompressedGRangesList")
-  RaggedExperiment(array.compartments, colData = colData(obj))
-}
-
-#' Preprocess arrays for compartment inference
-#'
-#' @name preprocessArrays
-#'
-#' @param obj Input SummarizedExperiment
-#' @param genome What genome are we working on ("hg19", "hg38", "mm9", "mm10")
-#' @param other Another arbitrary genome to compute compartments on
-#' @param array.type What type of array is this ("hm450", "EPIC")
-#'
-#' @return A preprocessed SummarizedExperiment to compute compartments
-#' @import SummarizedExperiment
-#'
-#' @examples
-#' if (requireNamespace("minfiData", quietly = TRUE)) {
-#'   grSet <- minfi::preprocessNoob(minfiData::RGsetEx.sub) |>
-#'     minfi::ratioConvert() |>
-#'     minfi::mapToGenome()
-#'   preprocessArrays(grSet)
-#' }
-#'
-#' @export
-preprocessArrays <- function(
-  obj,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  array.type = c("hm450", "EPIC")
-) {
-  if (!requireNamespace("minfi", quietly = TRUE)) {
-    stop("The minfi package must be installed for this functionality")
-  }
-
-  # what genome do we have
-  genome <- match.arg(genome)
-
-  # subset the array to open sea CpGs
-  obj.opensea <- filterOpenSea(obj, genome = genome, other = other)
-  verifyAssayNames(obj.opensea, assay = "array")
-
-  # convert to M-values if beta values given
-  # this should be default but allows handling if given M-values in Beta slot
-  is.beta <- min(assays(obj)$Beta, na.rm = TRUE) > 0
-  if (is.beta) {
-    message("Converting to squeezed M-values.")
-    assays(obj.opensea)$Beta <- flogit(assays(obj.opensea)$Beta)
-  }
-
-  # impute missing values if possible
-  if (any(is.na(minfi::getBeta(obj.opensea)))) {
-    message("Imputing missing values.")
-    obj.opensea <- imputeKNN(obj.opensea, assay = "array")
-  }
-
-  obj.opensea
-}
-
-
-# this is the main analysis function for computing compartments from arrays
-.arrayCompartments <- function(
-  obj,
-  original.obj,
-  res = 1e6,
-  chr = NULL,
-  targets = NULL,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  prior.means = NULL,
-  bootstrap = TRUE,
-  num.bootstraps = 1000,
-  parallel = FALSE,
-  cores = 2,
-  group = FALSE,
-  bootstrap.means = NULL
-) {
-  genome <- match.arg(genome)
-  if (parallel) options(mc.cores = cores)
-
-  # update
-  message("Computing compartments for ", chr)
-  obj <- keepSeqlevels(obj, chr, pruning.mode = "coarse")
-  original.obj <- keepSeqlevels(original.obj, chr, pruning.mode = "coarse")
-
-  # take care of the global means
-  if (!is.null(prior.means)) {
-    # this assumes that we've alread computed the global means
-    pmeans <- as(prior.means, "GRanges")
-    pmeans <- keepSeqlevels(pmeans, chr, pruning.mode = "coarse")
-    # go back to a matrix
-    prior.means <- as(pmeans, "matrix")
-    colnames(prior.means) <- "globalMean"
-  }
-
-  obj.bins <- shrinkBins(
-    obj,
-    original.obj,
-    prior.means = prior.means,
-    chr = chr,
-    res = res,
-    targets = targets,
-    assay = "array",
-    genome = genome,
-    jse = TRUE
-  )
-
-  obj.cor <- getCorMatrix(obj.bins, squeeze = !group)
-
-  if (any(is.na(obj.cor$binmat.cor))) {
-    obj.cor$gr$pc <- matrix(rep(NA, nrow(obj.cor$binmat.cor)))
-    obj.svd <- obj.cor$gr
-  } else {
-    # compute SVD of correlation matrix
-    obj.svd <- getABSignal(obj.cor, assay = "array")
-  }
-
-  if (!bootstrap) {
-    return(obj.svd)
-  }
-
-  # bootstrap the estimates
-  # always compute confidence intervals too
-  # take care of the global means
-  # this assumes that we've alread computed the global means
-  bmeans <- as(bootstrap.means, "GRanges")
-  bmeans <- keepSeqlevels(bmeans, chr, pruning.mode = "coarse")
-  # go back to a matrix
-  bmeans <- as(bmeans, "matrix")
-  colnames(bmeans) <- rep("globalMean", ncol(bmeans))
-
-  bootstrapCompartments(
-    obj,
-    original.obj,
-    bootstrap.samples = num.bootstraps,
-    chr = chr,
-    assay = "array",
-    parallel = parallel,
-    cores = cores,
-    targets = targets,
-    res = res,
-    genome = genome,
-    q = 0.95,
-    svd = obj.svd,
-    group = group,
-    bootstrap.means = bmeans
-  )
-}
diff --git a/R/getATACABsignal.R b/R/getCompartments.R
similarity index 54%
rename from R/getATACABsignal.R
rename to R/getCompartments.R
index ec6c19e1..ad8178d6 100644
--- a/R/getATACABsignal.R
+++ b/R/getCompartments.R
@@ -1,69 +1,28 @@
-#' @title Estimate A/B compartments from ATAC-seq data
-#'
-#' @description
-#' \code{getATACABsignal} returns estimated A/B compartments from ATAC-seq data.
-#'
-#' @param obj Input SummarizedExperiment object
-#' @param res Compartment resolution in bp
-#' @param parallel Whether to run samples in parallel
-#' @param chr What chromosome to work on (leave as NULL to run on all chromosomes)
-#' @param targets Samples/cells to shrink towards
-#' @param cores How many cores to use when running samples in parallel
-#' @param bootstrap Whether we should perform bootstrapping of inferred compartments
-#' @param num.bootstraps How many bootstraps to run
-#' @param genome What genome to work on ("hg19", "hg38", "mm9", "mm10")
-#' @param other Another arbitrary genome to compute compartments on
-#' @param group Whether to treat this as a group set of samples
-#' @param boot.parallel Whether to run the bootstrapping in parallel
-#' @param boot.cores How many cores to use for the bootstrapping
-#'
-#' @return A RaggedExperiment of inferred compartments
-#' @import SummarizedExperiment
-#' @import RaggedExperiment
-#' @importFrom parallel mclapply
-#' @importFrom methods as
-#' @export
-#'
-#' @aliases getRNAABsignal
-#'
-#' @examples
-#' if (requireNamespace("csaw", quietly = TRUE)) {
-#'   data("k562_scatac_chr14", package = "compartmap")
-#'   atac_compartments <- getATACABsignal(
-#'     k562_scatac_chr14,
-#'     parallel = FALSE,
-#'     chr = "chr14",
-#'     bootstrap = FALSE,
-#'     genome = "hg19",
-#'     group = TRUE
-#'   )
-#' }
-getATACABsignal <- function(
+getCompartments <- function(
   obj,
-  res = 1e6,
-  parallel = FALSE,
-  chr = NULL,
-  targets = NULL,
-  cores = 2,
-  bootstrap = TRUE,
-  num.bootstraps = 100,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  group = FALSE,
-  boot.parallel = FALSE,
-  boot.cores = 2
+  assay,
+  res,
+  parallel,
+  chr,
+  targets,
+  cores,
+  bootstrap,
+  num.bootstraps,
+  boot.parallel,
+  boot.cores,
+  genome,
+  group
 ) {
-  chr <- chr %||%
-    {
-      message("Processing all chromosomes")
-      getChrs(obj)
-    }
+  if (is.null(chr)) {
+    message("Assuming we want to process all chromosomes.")
+    chr <- getChrs(obj)
+  }
 
   if (is.null(colnames(obj))) stop("colnames needs to be sample names.")
   columns <- colnames(obj)
   names(columns) <- columns
 
-  prior.means <- getGlobalMeans(obj = obj, targets = targets, assay = "atac")
+  prior.means <- getGlobalMeans(obj = obj, targets = targets, assay = assay)
 
   if (bootstrap) {
     message("Pre-computing the bootstrap global means.")
@@ -71,17 +30,18 @@ getATACABsignal <- function(
       obj = obj,
       targets = targets,
       num.bootstraps = num.bootstraps,
-      assay = "atac",
+      assay = assay,
       parallel = parallel,
       num.cores = cores
     )
   }
 
   if (group) {
-    atac.compartments.list <- mclapply(chr, function(c) {
-      atacCompartments(
+    compartments.list <- mclapply(chr, function(c) {
+      .getCompartments(
         obj,
         obj,
+        assay = assay,
         res = res,
         chr = c,
         targets = targets,
@@ -96,18 +56,19 @@ getATACABsignal <- function(
       )
     }, mc.cores = ifelse(parallel, cores, 1))
 
-    atac.compartments <- sort(unlist(as(atac.compartments.list, "GRangesList")))
-    return(atac.compartments)
+    compartments <- sort(unlist(as(compartments.list, "GRangesList")))
+    return(compartments)
   }
 
-  atac.compartments <- mclapply(columns, function(s) {
+  compartments <- mclapply(columns, function(s) {
     obj.sub <- obj[, s]
 
     message("Working on ", s)
-    atac.compartments.list <- lapply(chr, function(c) {
-      atacCompartments(
+    compartments.list <- lapply(chr, function(c) {
+      .getCompartments(
         obj.sub,
         obj,
+        assay = assay,
         res = res,
         chr = c,
         targets = targets,
@@ -121,19 +82,18 @@ getATACABsignal <- function(
         bootstrap.means = bmeans
       )
     })
+    sort(unlist(as(compartments.list, "GRangesList")))
+  }, mc.cores = ifelse(parallel, cores, 1), mc.preschedule = F)
 
-    sort(unlist(as(atac.compartments.list, "GRangesList")))
-  }, mc.cores = ifelse(parallel, cores, 1))
-
-  atac.compartments <- as(atac.compartments, "CompressedGRangesList")
-  RaggedExperiment(atac.compartments, colData = colData(obj))
+  compartments <- as(compartments, "CompressedGRangesList")
+  RaggedExperiment(compartments, colData = colData(obj))
 }
 
-# worker function
-# this is the main analysis function for computing compartments from atacs
-atacCompartments <- function(
+# this is the main analysis function for computing compartments
+.getCompartments <- function(
   obj,
   original.obj,
+  assay,
   res = 1e6,
   chr = NULL,
   targets = NULL,
@@ -172,7 +132,7 @@ atacCompartments <- function(
     chr = chr,
     res = res,
     targets = targets,
-    assay = "atac",
+    assay = assay,
     genome = genome,
     jse = TRUE
   )
@@ -184,7 +144,7 @@ atacCompartments <- function(
     obj.svd <- obj.cor$gr
   } else {
     # compute SVD of correlation matrix
-    obj.svd <- getABSignal(obj.cor, assay = "atac")
+    obj.svd <- getABSignal(obj.cor, assay = assay)
   }
 
   if (!bootstrap) {
@@ -206,7 +166,7 @@ atacCompartments <- function(
     original.obj,
     bootstrap.samples = num.bootstraps,
     chr = chr,
-    assay = "atac",
+    assay = assay,
     parallel = parallel,
     cores = cores,
     targets = targets,
@@ -218,7 +178,3 @@ atacCompartments <- function(
     bootstrap.means = bmeans
   )
 }
-
-#' @describeIn getATACABsignal Alias for getATACABsignal
-#'
-getRNAABsignal <- getATACABsignal
diff --git a/R/plotAB.R b/R/plotAB.R
index b8d1566d..8b4db5b6 100644
--- a/R/plotAB.R
+++ b/R/plotAB.R
@@ -2,7 +2,7 @@
 #'
 #' Plot A/B compartments bins
 #'
-#' @param grAB              The GRanges object returned from scCompartments and getArrayABsignal
+#' @param grAB              The GRanges object returned from scCompartments and arrayCompartments
 #' @param chr               Chromosome to subset to for plotting
 #' @param main              Title for the plot
 #' @param ylim              Y-axis limits (default is -1 to 1)
diff --git a/R/preprocessArrays.R b/R/preprocessArrays.R
new file mode 100644
index 00000000..4e24d220
--- /dev/null
+++ b/R/preprocessArrays.R
@@ -0,0 +1,54 @@
+#' Preprocess arrays for compartment inference
+#'
+#' @name preprocessArrays
+#'
+#' @param obj Input SummarizedExperiment
+#' @param genome What genome are we working on ("hg19", "hg38", "mm9", "mm10")
+#' @param other Another arbitrary genome to compute compartments on
+#' @param array.type What type of array is this ("hm450", "EPIC")
+#'
+#' @return A preprocessed SummarizedExperiment to compute compartments
+#' @import SummarizedExperiment
+#'
+#' @examples
+#' if (requireNamespace("minfiData", quietly = TRUE)) {
+#'   grSet <- minfi::preprocessNoob(minfiData::RGsetEx.sub) |>
+#'     minfi::ratioConvert() |>
+#'     minfi::mapToGenome()
+#'   preprocessArrays(grSet)
+#' }
+#'
+#' @export
+preprocessArrays <- function(
+  obj,
+  genome = c("hg19", "hg38", "mm9", "mm10"),
+  other = NULL,
+  array.type = c("hm450", "EPIC")
+) {
+  if (!requireNamespace("minfi", quietly = TRUE)) {
+    stop("The minfi package must be installed for this functionality")
+  }
+
+  # what genome do we have
+  genome <- match.arg(genome)
+
+  # subset the array to open sea CpGs
+  obj.opensea <- filterOpenSea(obj, genome = genome, other = other)
+  verifyAssayNames(obj.opensea, assay = "array")
+
+  # convert to M-values if beta values given
+  # this should be default but allows handling if given M-values in Beta slot
+  is.beta <- min(assays(obj)$Beta, na.rm = TRUE) > 0
+  if (is.beta) {
+    message("Converting to squeezed M-values.")
+    assays(obj.opensea)$Beta <- flogit(assays(obj.opensea)$Beta)
+  }
+
+  # impute missing values if possible
+  if (any(is.na(minfi::getBeta(obj.opensea)))) {
+    message("Imputing missing values.")
+    obj.opensea <- imputeKNN(obj.opensea, assay = "array")
+  }
+
+  obj.opensea
+}
diff --git a/R/scCompartments.R b/R/scCompartments.R
index 050b24bb..251bb099 100644
--- a/R/scCompartments.R
+++ b/R/scCompartments.R
@@ -1,16 +1,18 @@
-#' @title Estimate A/B compartments from single-cell sequencing data
+#' @title Estimate A/B compartments from single-cell RNA or ATAC sequencing data
 #'
 #' @description
 #' \code{scCompartments} returns estimated A/B compartments from sc-seq data.
 #'
 #' @param obj Input SummarizedExperiment object
 #' @param res Compartment resolution in bp
-#' @param parallel Whether to run samples in parallel
 #' @param chr What chromosome to work on (leave as NULL to run on all chromosomes)
 #' @param targets Samples/cells to shrink towards
+#' @param parallel Whether to run samples in parallel
 #' @param cores How many cores to use when running samples in parallel
 #' @param bootstrap Whether we should perform bootstrapping of inferred compartments
 #' @param num.bootstraps How many bootstraps to run
+#' @param boot.parallel Whether to run the bootstrapping in parallel
+#' @param boot.cores How many cores to use for the bootstrapping
 #' @param genome What genome to work on ("hg19", "hg38", "mm9", "mm10")
 #' @param group Whether to treat this as a group set of samples
 #' @param assay What type of single-cell assay is the input data ("atac" or "rna")
@@ -24,20 +26,22 @@
 #' data("k562_scrna_chr14", package = "compartmap")
 #' sc_compartments <- scCompartments(
 #'   k562_scrna_chr14,
-#'   parallel = FALSE,
 #'   chr = "chr14",
+#'   parallel = FALSE,
 #'   bootstrap = FALSE,
 #'   genome = "hg19"
 #' )
 scCompartments <- function(
   obj,
   res = 1e6,
-  parallel = FALSE,
   chr = NULL,
   targets = NULL,
+  parallel = FALSE,
   cores = 2,
   bootstrap = TRUE,
   num.bootstraps = 100,
+  boot.parallel = FALSE,
+  boot.cores = 2,
   genome = c("hg19", "hg38", "mm9", "mm10"),
   group = FALSE,
   assay = c("atac", "rna")
@@ -49,18 +53,19 @@ scCompartments <- function(
   if (!all(assay %in% c("atac", "rna"))) stop("Supported assays are 'atac', and 'rna'.")
   assay <- tolower(match.arg(assay))
   verifyAssayNames(obj, assay = assay)
-
-  sc_compartments <- getATACABsignal(
+  getCompartments(
     obj = obj,
+    assay = assay,
     res = res,
-    parallel = parallel,
     chr = chr,
     targets = targets,
+    parallel = parallel,
     cores = cores,
     bootstrap = bootstrap,
     num.bootstraps = num.bootstraps,
+    boot.parallel = boot.parallel,
+    boot.cores = boot.cores,
     genome = genome,
     group = group
   )
-  return(sc_compartments)
 }
diff --git a/man/getArrayABsignal.Rd b/man/arrayCompartments.Rd
similarity index 84%
rename from man/getArrayABsignal.Rd
rename to man/arrayCompartments.Rd
index 330db367..29fcb711 100644
--- a/man/getArrayABsignal.Rd
+++ b/man/arrayCompartments.Rd
@@ -1,25 +1,25 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getArrayABsignal.R
-\name{getArrayABsignal}
-\alias{getArrayABsignal}
+% Please edit documentation in R/arrayCompartments.R
+\name{arrayCompartments}
+\alias{arrayCompartments}
 \title{Estimate A/B compartments from methylation array data}
 \usage{
-getArrayABsignal(
+arrayCompartments(
   obj,
   res = 1000000,
-  parallel = TRUE,
   chr = NULL,
   targets = NULL,
   preprocess = TRUE,
+  parallel = TRUE,
   cores = 2,
   bootstrap = TRUE,
   num.bootstraps = 1000,
+  boot.parallel = TRUE,
+  boot.cores = 2,
   genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  array.type = c("hm450", "EPIC"),
   group = FALSE,
-  boot.parallel = TRUE,
-  boot.cores = 2
+  other = NULL,
+  array.type = c("hm450", "EPIC")
 )
 }
 \arguments{
@@ -27,46 +27,46 @@ getArrayABsignal(
 
 \item{res}{Compartment resolution in bp}
 
-\item{parallel}{Whether to run samples in parallel}
-
 \item{chr}{What chromosome to work on (leave as NULL to run on all chromosomes)}
 
 \item{targets}{Samples/cells to shrink towards}
 
 \item{preprocess}{Whether to preprocess the arrays prior to compartment inference}
 
+\item{parallel}{Whether to run samples in parallel}
+
 \item{cores}{How many cores to use when running samples in parallel}
 
 \item{bootstrap}{Whether we should perform bootstrapping of inferred compartments}
 
 \item{num.bootstraps}{How many bootstraps to run}
 
-\item{genome}{What genome to work on ("hg19", "hg38", "mm9", "mm10")}
+\item{boot.parallel}{Whether to run the bootstrapping in parallel}
 
-\item{other}{Another arbitrary genome to compute compartments on}
+\item{boot.cores}{How many cores to use for the bootstrapping}
 
-\item{array.type}{What type of array is this ("hm450", "EPIC")}
+\item{genome}{What genome to work on ("hg19", "hg38", "mm9", "mm10")}
 
 \item{group}{Whether to treat this as a group set of samples}
 
-\item{boot.parallel}{Whether to run the bootstrapping in parallel}
+\item{other}{Another arbitrary genome to compute compartments on}
 
-\item{boot.cores}{How many cores to use for the bootstrapping}
+\item{array.type}{What type of array is this ("hm450", "EPIC")}
 }
 \value{
 A RaggedExperiment of inferred compartments
 }
 \description{
-\code{getArrayABsignal} returns estimated A/B compartments from methylation array data.
+\code{arrayCompartments} returns estimated A/B compartments from methylation array data.
 }
 \examples{
 
 if (requireNamespace("minfi", quietly = TRUE)) {
   data("array_data_chr14", package = "compartmap")
-  array_compartments <- getArrayABsignal(
+  array_compartments <- arrayCompartments(
     array.data.chr14,
-    parallel=FALSE,
     chr="chr14",
+    parallel=FALSE,
     bootstrap=FALSE,
     genome="hg19",
     array.type="hm450"
diff --git a/man/getATACABsignal.Rd b/man/getATACABsignal.Rd
deleted file mode 100644
index 3a9c419c..00000000
--- a/man/getATACABsignal.Rd
+++ /dev/null
@@ -1,90 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getATACABsignal.R
-\name{getATACABsignal}
-\alias{getATACABsignal}
-\alias{getRNAABsignal}
-\title{Estimate A/B compartments from ATAC-seq data}
-\usage{
-getATACABsignal(
-  obj,
-  res = 1000000,
-  parallel = FALSE,
-  chr = NULL,
-  targets = NULL,
-  cores = 2,
-  bootstrap = TRUE,
-  num.bootstraps = 100,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  group = FALSE,
-  boot.parallel = FALSE,
-  boot.cores = 2
-)
-
-getRNAABsignal(
-  obj,
-  res = 1000000,
-  parallel = FALSE,
-  chr = NULL,
-  targets = NULL,
-  cores = 2,
-  bootstrap = TRUE,
-  num.bootstraps = 100,
-  genome = c("hg19", "hg38", "mm9", "mm10"),
-  other = NULL,
-  group = FALSE,
-  boot.parallel = FALSE,
-  boot.cores = 2
-)
-}
-\arguments{
-\item{obj}{Input SummarizedExperiment object}
-
-\item{res}{Compartment resolution in bp}
-
-\item{parallel}{Whether to run samples in parallel}
-
-\item{chr}{What chromosome to work on (leave as NULL to run on all chromosomes)}
-
-\item{targets}{Samples/cells to shrink towards}
-
-\item{cores}{How many cores to use when running samples in parallel}
-
-\item{bootstrap}{Whether we should perform bootstrapping of inferred compartments}
-
-\item{num.bootstraps}{How many bootstraps to run}
-
-\item{genome}{What genome to work on ("hg19", "hg38", "mm9", "mm10")}
-
-\item{other}{Another arbitrary genome to compute compartments on}
-
-\item{group}{Whether to treat this as a group set of samples}
-
-\item{boot.parallel}{Whether to run the bootstrapping in parallel}
-
-\item{boot.cores}{How many cores to use for the bootstrapping}
-}
-\value{
-A RaggedExperiment of inferred compartments
-}
-\description{
-\code{getATACABsignal} returns estimated A/B compartments from ATAC-seq data.
-}
-\section{Functions}{
-\itemize{
-\item \code{getRNAABsignal()}: Alias for getATACABsignal
-
-}}
-\examples{
-if (requireNamespace("csaw", quietly = TRUE)) {
-  data("k562_scatac_chr14", package = "compartmap")
-  atac_compartments <- getATACABsignal(
-    k562_scatac_chr14,
-    parallel = FALSE,
-    chr = "chr14",
-    bootstrap = FALSE,
-    genome = "hg19",
-    group = TRUE
-  )
-}
-}
diff --git a/man/plotAB.Rd b/man/plotAB.Rd
index ad420e8a..10dae644 100644
--- a/man/plotAB.Rd
+++ b/man/plotAB.Rd
@@ -20,7 +20,7 @@ plotAB(
 )
 }
 \arguments{
-\item{grAB}{The GRanges object returned from scCompartments and getArrayABsignal}
+\item{grAB}{The GRanges object returned from scCompartments and arrayCompartments}
 
 \item{chr}{Chromosome to subset to for plotting}
 
diff --git a/man/preprocessArrays.Rd b/man/preprocessArrays.Rd
index 972260f5..a040ad43 100644
--- a/man/preprocessArrays.Rd
+++ b/man/preprocessArrays.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getArrayABsignal.R
+% Please edit documentation in R/preprocessArrays.R
 \name{preprocessArrays}
 \alias{preprocessArrays}
 \title{Preprocess arrays for compartment inference}
diff --git a/man/scCompartments.Rd b/man/scCompartments.Rd
index acaff07e..92193fcb 100644
--- a/man/scCompartments.Rd
+++ b/man/scCompartments.Rd
@@ -2,17 +2,19 @@
 % Please edit documentation in R/scCompartments.R
 \name{scCompartments}
 \alias{scCompartments}
-\title{Estimate A/B compartments from single-cell sequencing data}
+\title{Estimate A/B compartments from single-cell RNA or ATAC sequencing data}
 \usage{
 scCompartments(
   obj,
   res = 1000000,
-  parallel = FALSE,
   chr = NULL,
   targets = NULL,
+  parallel = FALSE,
   cores = 2,
   bootstrap = TRUE,
   num.bootstraps = 100,
+  boot.parallel = FALSE,
+  boot.cores = 2,
   genome = c("hg19", "hg38", "mm9", "mm10"),
   group = FALSE,
   assay = c("atac", "rna")
@@ -23,18 +25,22 @@ scCompartments(
 
 \item{res}{Compartment resolution in bp}
 
-\item{parallel}{Whether to run samples in parallel}
-
 \item{chr}{What chromosome to work on (leave as NULL to run on all chromosomes)}
 
 \item{targets}{Samples/cells to shrink towards}
 
+\item{parallel}{Whether to run samples in parallel}
+
 \item{cores}{How many cores to use when running samples in parallel}
 
 \item{bootstrap}{Whether we should perform bootstrapping of inferred compartments}
 
 \item{num.bootstraps}{How many bootstraps to run}
 
+\item{boot.parallel}{Whether to run the bootstrapping in parallel}
+
+\item{boot.cores}{How many cores to use for the bootstrapping}
+
 \item{genome}{What genome to work on ("hg19", "hg38", "mm9", "mm10")}
 
 \item{group}{Whether to treat this as a group set of samples}
@@ -51,8 +57,8 @@ A RaggedExperiment of inferred compartments
 data("k562_scrna_chr14", package = "compartmap")
 sc_compartments <- scCompartments(
   k562_scrna_chr14,
-  parallel = FALSE,
   chr = "chr14",
+  parallel = FALSE,
   bootstrap = FALSE,
   genome = "hg19"
 )
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 62946a52..c1e753db 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -23,14 +23,13 @@ reference:
 - title: Compartment mapping
   contents:
     - scCompartments
-    - getArrayABsignal
+    - arrayCompartments
 - title: Compartment helper
   contents:
     - filterCompartments
     - fixCompartments
     - extractOpenClosed
     - getABSignal
-    - getATACABsignal
     - getRNAABsignal
 - title: Correlation matrix
   contents:
diff --git a/tests/testthat/test-getArrayABsignal.R b/tests/testthat/test-getArrayABsignal.R
index f4ded02d..07696f14 100644
--- a/tests/testthat/test-getArrayABsignal.R
+++ b/tests/testthat/test-getArrayABsignal.R
@@ -1,10 +1,10 @@
 se.noranges <- SummarizedExperiment(rowRanges = GRanges())
 se.bad <- SummarizedExperiment(rowRanges = GRanges("chr1:1-10"), assays = SimpleList(a = matrix()))
 
-test_that("getArrayABsignal bad inputs", {
-  expect_error(getArrayABsignal(iris), err.verifySE)
-  expect_error(getArrayABsignal(se.noranges), err.verifyCoords)
-  expect_error(getArrayABsignal(se.bad), err.verifyAssayNames.beta)
+test_that("arrayCompartments bad inputs", {
+  expect_error(arrayCompartments(iris), err.verifySE)
+  expect_error(arrayCompartments(se.noranges), err.verifyCoords)
+  expect_error(arrayCompartments(se.bad), err.verifyAssayNames.beta)
 })
 
 test_that(".preprocessArrays", {