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

## Documentation for package ‘ELViS’ version 1.1.9

- 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