ct.viewGuides: Generate a Plot of individual gRNA Pair Data in a Crispr...

In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description

This function generates a visualization of the effect estimates from a MArrayLM model result for all of the individual guides targeting a particular element, specified somewhere in the library annotation file. The estimated effect size and variance is plotted relative to zero for the specified contrast, with the color of the dot indicating the relative scale of the of the guide intercept within the model framework, with warmer colors indicating lowly expressed guides. For comparison, the density of gRNA fold change estimates is privided in a pane on the right, with white lines indicating the exact levels of the individual guides.

Usage

ct.viewGuides(
  gene,
  fit,
  ann,
  type = "geneSymbol",
  contrast.term = NULL,
  ylims = NULL
)

Arguments

gene	the name of the target element of interest, contained within the "type" column of the annotation file.
fit	An object of class MArrayLM containing, at minimum, an "Amean" slot containing the guide level abundances, a "coefficients" slot containing the effect estimates for each guide, and an "stdev.unscaled" slot giving the coefficient standard Deviations.
ann	A data.frame object containing the gRNA annotations. At mimimum, it should have a column with the name specified by the type argument, containing the element targeted by each guide.
type	A character string indicating the column in ann containing the target of interest.
contrast.term	If a fit object with multiple coefficients is passed in, a string indiating the coefficient of interest.
ylims	An optional numeric vector of length 2 indicating the extremes of the y-axis scale.

Value

An image summarizing gRNA behavior within the specifed gene on the default device.

Author(s)

Russell Bainer

Examples

data('fit')
data('ann')
ct.viewGuides('Target1633', fit, ann)

gCrisprTools documentation built on Nov. 8, 2020, 8:17 p.m.