Package index

All functions

example_nsig_df

Example normal signal matrix file

example_pif

Example Probe Information File

example_sif

Example Sample Information File

example_tsig_df

Example tumor signal matrix file

filter_blacklist()

Filter out common germline copy-number variants

hg19_blacklist

Germline Copy Number Variants Blacklist Data Version hg19

hg38_blacklist

Germline Copy Number Variants Blacklist Data Version hg38

plot_latent_factor_importance()

Plot importance of latent factors

plot_signal_along_loci()

Plot signal along genome before and after TangentXY normalization

plot_signal_noise()

Plot signal and noise before and after TangentXY normalization

run_cbs()

Run CBS segmentation on normalized tumor signals

run_pseudotangent()

Run the PseudoTangentXY algorithm

run_tangent()

Run the TangentXY algorithm

save_segmentation()

Save segmentation file