An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

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Documentation for package ‘ELViS’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ELViS-package	ELViS : An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile.
coord_to_grng	Convert coordinate string to grng object
coord_to_lst	Convert coordinate string to list of chr,start and end
depth_hist	Sample filtering threshold examination plot.
ELViS	ELViS : An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile.
ELViS_toy_run_result	ELViS Toy Example - Run Result
filt_samples	Filtering samples based on summary statistic
gene_cn_heatmaps	Gene Copy Number Heatmap
get_depth_matrix	Generate a read depth matrix of positions x samples from input BAM files list
get_new_baseline	Get new baselines according to criteria user designates
integrative_heatmap	Plot heatmaps based on simple integrative clustering of multiple matrices
mtrx_samtools_reticulate	ELViS Toy Example - Base-Resolution Raw Read Depth
norm_fun	Normalization - scaling by certain quantile
plot_pileUp_multisample	Get a list of pile-up plots over multiple samples
run_ELViS	Run ELViS using input raw depth matrix
total_aligned_base__host_and_virus	ELViS Toy Example - Total Aligned Base
toy_example	ELViS Toy Example - Metadata