Estimate A/B compartments from methylation array data

getArrayABsignal returns estimated A/B compartments from methylation array data.

Usage

getArrayABsignal(
  obj,
  res = 1000000,
  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
)

Arguments

obj: Input SummarizedExperiment object
res: Compartment resolution in bp
parallel: Whether to run samples in parallel
chr: What chromosome to work on (leave as NULL to run on all chromosomes)
targets: Samples/cells to shrink towards
preprocess: Whether to preprocess the arrays prior to compartment inference
cores: How many cores to use when running samples in parallel
bootstrap: Whether we should perform bootstrapping of inferred compartments
num.bootstraps: How many bootstraps to run
genome: What genome to work on ("hg19", "hg38", "mm9", "mm10")
other: Another arbitrary genome to compute compartments on
array.type: What type of array is this ("hm450", "EPIC")
group: Whether to treat this as a group set of samples
boot.parallel: Whether to run the bootstrapping in parallel
boot.cores: How many cores to use for the bootstrapping

Value

A RaggedExperiment of inferred compartments

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"
  )
}
#> Filtering to open sea CpG loci...
#> Converting to squeezed M-values.
#> Imputing missing values.
#> Dropping samples with >80% NAs.
#> Imputing missing data with kNN.
#> Cluster size 3332 broken into 518 2814 
#> Done cluster 518 
#> Cluster size 2814 broken into 969 1845 
#> Done cluster 969 
#> Cluster size 1845 broken into 600 1245 
#> Done cluster 600 
#> Done cluster 1245 
#> Done cluster 1845 
#> Done cluster 2814 
#> Working on naive.1
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on rTreg.2
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on act_naive.3
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on naive.4
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on act_naive.5
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on act_rTreg.6
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on naive.7
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on rTreg.8
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on act_naive.9
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on act_rTreg.10
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.
#> Working on birth.11
#> Computing compartments for chr14
#> Number of means fewer than 4. Using Bayes instead of JSE.
#> 108 bins created...
#> Calculating correlations...
#> Done...
#> Calculating eigenvectors.
#> Smoothing eigenvector.
#> Done smoothing.