allele_effect_plot

Result from a call to deletion_analysis.

del_result

Window on either size of the CRISPR cut site to show in the plot.

viewing_window

The maximum number of alleles to show in the plot.

max_alleles

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

The R package for GenIE analysis is designed to analyze the next-generation sequencing
output from a set of GenIE experimental replicates. GenIE (genome-editing interrogation of enhancers)
is an experimental method to evaluate the effects of individual single-nucleotide polymorphisms (SNPs)
on gene transcription. It is based on targeted CRISPR-Cas9 genome editing in cultured cells to
produce indels at a target locus, optionally with a homology-dependent recombination (HDR) construct
to create precisely defined genomic changes. Following this, both genomic DNA (gDNA) and RNA are
extracted from the same pool of cells, then complementary DNA (cDNA) is generated from the RNA. Both
gDNA and cDNA are amplified with locus-specific PCR primers, in multiple replicates, and libraries of
the experimental replicates are prepared for next-generation sequencing. The sequencing data from each
replicate for each region should be aligned to either the full reference genome or to a locus-specific
(amplicon) reference genome for analysis by 'rgenie'.

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

Description

Usage

Arguments

Value

See Also

Examples