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rgenie

rgenie is an R package to analyze the sequencing output from a set of GenIE experimental replicates.

Installation

If you don't have devtools yet, first install devtools:

install.packages("devtools")

Then install rgenie using devtools:

devtools::install_github("jeremy37/rgenie")

Overview

GenIE (genome-editing interrogation of enhancers) is an experimental method to evaluate the effects of individual SNPs on gene transcription.

Briefly, CRISPR-Cas9 is targeted near a SNP of interest, and typically an oligonucleotide for homology-directed repair (HDR) will be included. With the editing done in a pool of cells, the single nucleotide change can be achieved in a fraction of cell chromosomes, and the remaining chromosomes will either be wild-type or will have deletions in the region. You then extract both RNA and DNA from the pool of cells, and do multiple replicates to amplify an amplicon from each of these (genomic DNA and cDNA). rgenie can help to visualize the experiment and compute statistics for the effects of different alleles on gene transcription.

The plot below shows the set of alleles measured in a set of gDNA and cDNA replicates.

Getting started

The Introductory vignette shows how to download example data and run an analysis.

The rgenie in depth vignette provides more details on the parameters for some methods and how to interpret results.

Citation

Cooper SE, Schwartzentruber J, Bello E, Coomber EL, Bassett AR. Screening for functional transcriptional and splicing regulatory variants with GenIE. Not yet published.

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Version

Install

install.packages('rgenie')

Monthly Downloads

4

Version

1.0.0

License

MIT + file LICENSE

Issues

2

Pull Requests

0

Stars

2

Forks

0

Maintainer

Jeremy Schwartzentruber

Last Published

September 30th, 2020

Functions in rgenie (1.0.0)

deletion_summary_plot

Plots a summary of deletion analysis results for a single region.
bind_results

Given results for rgenie grep or deletion analysis of a set of regions, merges together tables across regions.
download_example

Downloads example data for rgenie.
deletion_plots

Returns all main plots for a single deletion analysis result.
experiment_summary_plot

Plots a summary of genie results across multiple regions.
allele_effect_plot

Plots estimated effect sizes and confidence intervals for top alleles from a deletion analysis.
deletion_analysis

Alignment-based GenIE analysis
deletion_alleles_plot

Plots unique deletion alleles and their "pileup" count profile separately for cDNA and gDNA.
deletion_profile_plot

Plots the deletion "pileup" profile separately for each replicate.
genie_plot_options

Returns a list with default options for all rgenie plots, useful in calls to deletion_plots().
get_variance_components

Performs a variance components estimate for each deletion allele based on the replicate metadata provided.
mul1_del_results

GenIE replicates for the MUL1 example.
grep_summary_plot

Plots a summary of genie results from a grep analysis.
variance_components_plot

Plots variance components estimates for all unique alleles.
grep_analysis

Grep-based GenIE analysis
mul1_regions

GenIE regions for the MUL1 example.
power_plots

Returns a set of plots summarising the expected power to detect a significant effect given various allele fraction and effect size combinations.
mul1_grep_results

GenIE grep results list.
replicate_qc_plot

Plots quality control metrics for deletion analysis replicates.
rgenie

rgenie: Analysis of GenIE experiments
replicate_summary_plot

Plots a summary of deletion analysis replicates.
mul1_replicates

GenIE replicates for the MUL1 example.
power_analysis

Performs estimates of power to detect effects of alleles at different read fractions, given the variance observed in the del_result replicates.