Estimate A/B compartments from single-cell sequencing data

scCompartments returns estimated A/B compartments from sc-seq data.

Usage

scCompartments(
  obj,
  res = 1000000,
  parallel = FALSE,
  chr = NULL,
  targets = NULL,
  cores = 2,
  bootstrap = TRUE,
  num.bootstraps = 100,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  group = FALSE,
  assay = c("atac", "rna")
)

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
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")
group: Whether to treat this as a group set of samples
assay: What type of single-cell assay is the input data ("atac" or "rna")

Value

A RaggedExperiment of inferred compartments

Examples

data("k562_scrna_chr14", package = "compartmap")
sc_compartments <- scCompartments(
  k562_scrna_chr14,
  parallel = FALSE,
  chr = "chr14",
  bootstrap = FALSE,
  genome = "hg19"
)
#> Working on A10_hg19Aligned.sortedByCoord.out.bw
#> 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 A2_hg19Aligned.sortedByCoord.out.bw
#> 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 A3_hg19Aligned.sortedByCoord.out.bw
#> 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 A4_hg19Aligned.sortedByCoord.out.bw
#> 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 A5_hg19Aligned.sortedByCoord.out.bw
#> 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 A6_hg19Aligned.sortedByCoord.out.bw
#> 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 A7_hg19Aligned.sortedByCoord.out.bw
#> 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 A8_hg19Aligned.sortedByCoord.out.bw
#> 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 A9_hg19Aligned.sortedByCoord.out.bw
#> 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 B1_hg19Aligned.sortedByCoord.out.bw
#> 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 B2_hg19Aligned.sortedByCoord.out.bw
#> 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 B3_hg19Aligned.sortedByCoord.out.bw
#> 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 B4_hg19Aligned.sortedByCoord.out.bw
#> 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 B5_hg19Aligned.sortedByCoord.out.bw
#> 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 B6_hg19Aligned.sortedByCoord.out.bw
#> 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 B7_hg19Aligned.sortedByCoord.out.bw
#> 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 B8_hg19Aligned.sortedByCoord.out.bw
#> 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 B9_hg19Aligned.sortedByCoord.out.bw
#> 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 C1_hg19Aligned.sortedByCoord.out.bw
#> 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 C2_hg19Aligned.sortedByCoord.out.bw
#> 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 C3_hg19Aligned.sortedByCoord.out.bw
#> 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 C4_hg19Aligned.sortedByCoord.out.bw
#> 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 C5_hg19Aligned.sortedByCoord.out.bw
#> 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 C6_hg19Aligned.sortedByCoord.out.bw
#> 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 C7_hg19Aligned.sortedByCoord.out.bw
#> 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 C8_hg19Aligned.sortedByCoord.out.bw
#> 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 C9_hg19Aligned.sortedByCoord.out.bw
#> 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 D1_hg19Aligned.sortedByCoord.out.bw
#> 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 D2_hg19Aligned.sortedByCoord.out.bw
#> 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 D3_hg19Aligned.sortedByCoord.out.bw
#> 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 D4_hg19Aligned.sortedByCoord.out.bw
#> 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 D5_hg19Aligned.sortedByCoord.out.bw
#> 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 D6_hg19Aligned.sortedByCoord.out.bw
#> 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 D7_hg19Aligned.sortedByCoord.out.bw
#> 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 D8_hg19Aligned.sortedByCoord.out.bw
#> 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 E1_hg19Aligned.sortedByCoord.out.bw
#> 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 E2_hg19Aligned.sortedByCoord.out.bw
#> 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 E3_hg19Aligned.sortedByCoord.out.bw
#> 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 E4_hg19Aligned.sortedByCoord.out.bw
#> 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 E5_hg19Aligned.sortedByCoord.out.bw
#> 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 E6_hg19Aligned.sortedByCoord.out.bw
#> 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 E7_hg19Aligned.sortedByCoord.out.bw
#> 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 E8_hg19Aligned.sortedByCoord.out.bw
#> 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 E9_hg19Aligned.sortedByCoord.out.bw
#> 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 F1_hg19Aligned.sortedByCoord.out.bw
#> 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 F2_hg19Aligned.sortedByCoord.out.bw
#> 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 F3_hg19Aligned.sortedByCoord.out.bw
#> 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 F4_hg19Aligned.sortedByCoord.out.bw
#> 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 F5_hg19Aligned.sortedByCoord.out.bw
#> 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 F6_hg19Aligned.sortedByCoord.out.bw
#> 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 F7_hg19Aligned.sortedByCoord.out.bw
#> 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 F8_hg19Aligned.sortedByCoord.out.bw
#> 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 F9_hg19Aligned.sortedByCoord.out.bw
#> 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 G1_hg19Aligned.sortedByCoord.out.bw
#> 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 G2_hg19Aligned.sortedByCoord.out.bw
#> 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 G3_hg19Aligned.sortedByCoord.out.bw
#> 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 G4_hg19Aligned.sortedByCoord.out.bw
#> 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 G5_hg19Aligned.sortedByCoord.out.bw
#> 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 G6_hg19Aligned.sortedByCoord.out.bw
#> 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 G7_hg19Aligned.sortedByCoord.out.bw
#> 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 G8_hg19Aligned.sortedByCoord.out.bw
#> 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 G9_hg19Aligned.sortedByCoord.out.bw
#> 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 H1_hg19Aligned.sortedByCoord.out.bw
#> 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 H2_hg19Aligned.sortedByCoord.out.bw
#> 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 H3_hg19Aligned.sortedByCoord.out.bw
#> 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 H4_hg19Aligned.sortedByCoord.out.bw
#> 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 H5_hg19Aligned.sortedByCoord.out.bw
#> 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 H6_hg19Aligned.sortedByCoord.out.bw
#> 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 H7_hg19Aligned.sortedByCoord.out.bw
#> 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 H8_hg19Aligned.sortedByCoord.out.bw
#> 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.