A normalization and copy number estimation method for single-cell DNA sequencing


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Documentation for package ‘SCOPE’ version 1.20.0

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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