combine .atacCompartments and arrayCompartments workers into getCompartments

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)

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
+  )
+}