ct.scatter {gCrisprTools} | R Documentation

## 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)

[Package gCrisprTools version 2.0.0 Index]