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ABEMUS

Platform specific and data informed detection of somatic SNVs in cfDNA

Documentation

Visit project Wiki for full abemus documentation.

Quick start

1. Install abemus R package:
# from CRAN
install.packages('abemus')

# from github
library( "devtools" )
devtools::install_github("cibiobcg/abemus", build_vignettes = T)
2. Explore abemus utilities by following Usage steps as reported in the example workflow.

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Version

Install

install.packages('abemus')

Monthly Downloads

12

Version

1.0.2

License

GPL-3

Maintainer

Nicola Casiraghi

Last Published

December 18th, 2019

Functions in abemus (1.0.2)

apply_scaling_factor

Apply the scaling factor R to get the most suitable locus-specific AF threshold.
tab_optimal_R

[data] Summary table to select the best scaling factor R
split_pacbam_bychrom

Split PaCBAM ouputs by chromosomes
get_target_size

Compute total number of loci covered in a BED file
callsnvs

Call somatic SNVs by using both global and local error models
abemus

ABEMUS: Adaptive per Base Error Model in Ultra-deep Sequencing Data
bombanel_tab_cov_pbem

[data] Matrix of pbem thresholds
compute_pbem

Compute the per-base error measure (pbem) for each targeted locus and save allelic (AF) by bins of coverage.
get_case_mean_coverage

Compute the mean coverage of a CASE sample
bombanel_covs

[data] Coverage levels from simulated data
bed2positions

Unwrap a list of genomic intervals into a list of loci grouped by chromosome.
compute_afthreshold

Compute coverage-based and not-coverage-based allelic fraction thresholds
bombanel_afs

[data] Allelic Fractions from simulated data