getATACABsignal {compartmap} | R Documentation |
getATACABsignal
returns estimated A/B compartments from ATAC-seq data.
getATACABsignal( obj, res = 1e+06, 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 = 1e+06, 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 )
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") |
other |
Another arbitrary genome to compute compartments on |
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 |
A RaggedExperiment of inferred compartments
getRNAABsignal
: Alias for getATACABsignal
data("k562_scatac_chr14", package = "compartmap") atac_compartments <- getATACABsignal(k562_scatac_chr14, parallel=FALSE, chr="chr14", bootstrap=FALSE, genome="hg19", group = TRUE)