coverageObj.scopeDemo |
Pre-stored coverageObj.scope data for demonstration purposes |
get_bam_bed |
Get bam file directories, sample names, and whole genomic bins |
get_coverage_scDNA |
Get read coverage from single-cell DNA sequencing |
get_gc |
Compute GC content |
get_gini |
Compute Gini coefficients for single cells |
get_mapp |
Compute mappability |
get_samp_QC |
Get QC metrics for single cells |
iCN_sim |
A post cross-sample segmentation integer copy number matrix returned by SCOPE in the demo |
initialize_ploidy |
Ploidy pre-initialization |
initialize_ploidy_group |
Group-wise ploidy pre-initialization |
normalize_codex2_ns_noK |
Normalization of read depth without latent factors under the case-control setting |
normalize_scope |
Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control setting |
normalize_scope_foreach |
Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control setting in parallel |
normalize_scope_group |
Group-wise normalization of read depth with latent factors using Expectation-Maximization algorithm and shared clonal memberships |
normObj.scopeDemo |
Pre-stored normObj.scope data for demonstration purposes |
perform_qc |
Quality control for cells and bins |
plot_EM_fit |
Visualize EM fitting for each cell. |
plot_iCN |
Plot post-segmentation copy number profiles of integer values |
QCmetric.scopeDemo |
Pre-stored QCmetric data for demonstration purposes |
ref.scopeDemo |
Pre-stored 500kb-size reference genome for demonstration purposes |
ref_sim |
A reference genome in the toy dataset |
segment_CBScs |
Cross-sample segmentation |
Y_sim |
A read count matrix in the toy dataset |