scCompartments {compartmap} | R Documentation |
scCompartments
returns estimated A/B compartments from sc-seq data.
scCompartments( obj, res = 1e+06, 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") )
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") |
A RaggedExperiment of inferred compartments
data("k562_scrna_chr14", package = "compartmap") sc_compartments <- scCompartments(k562_scrna_chr14, parallel=FALSE, chr="chr14", bootstrap=FALSE, genome="hg19")