ct.scatter: Compare Two CRISPR Screen Contrasts via a Scatter Plot

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

Compare Two CRISPR Screen Contrasts via a Scatter Plot

Description

This is a function for comparing the results of two screening experiments. Given two summaryDF, the function places them in register with one another, generates a simplified scatter plot where enrichment or depletion in each contrast is represented by the associated "signed" log10 (*P*/*Q*)-value (where enriched signals are represented in the positive direction and depleted signals are shown in the negative direction), and returns an invisible 'data.frame' containing the target X-axis and Y-axis coordinates and corresponding quadrant.

This is a target-level analysis, and some minor simplifications are introduced to screen signals for the sake of clarity. Principal among these is the decision to collapse gene signals to a single directional enrichment statistic. Target-level signals are typically aggregates of many guide-level signals, it is formally possible for targets to be both significantly enriched and significantly depleted within a single screen contrast as a result of substantially divergent reagent activity. This behavior is uncommon, however, and so targets are represented by selecting the direction of enrichment or depletion associated with the most significant (*P*/*Q*)-value. This directionality is then encoded into the X-axis and Y-axis position of the target as the sign of the signal as described above.

Usage

ct.scatter(
  dflist,
  targets = c("geneSymbol", "geneID"),
  statistic = c("best.p", "best.q"),
  cutoff = 0.05,
  plot.it = TRUE
)

Arguments

dflist	A (named) list of results dataframes, of length 2. See ct.generateResults.
targets	Column of the provided summaryDF to consider. Must be geneID or geneSymbol.
statistic	Statistic to plot on each axis (after -log10 transformation). Must be 'p', 'q', or 'rho'.
cutoff	significance cutoff used to define the significance quadrants (cannot be exactly zero).
plot.it	Logical indicating whether to compose the plot on the default device.

Value

Invisibly, a list of length 4 containing the genes passing significance for the respective quadrants.

Author(s)

Russell Bainer

Examples

data('resultsDF')
scat <- ct.scatter(list('FirstResult' = resultsDF[100:2100,], 'SecondResult' = resultsDF[1:2000,]))
head(scat)

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.