plot_cooks_vs_wald: Compare Cook's distances to Wald statistic ranks

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Compare Cook's distances to Wald statistic ranks

Description

Plot max Cook's distances per feature vs. Wald statistic rankings.

Usage

plot_cooks_vs_wald(
  dds_fit,
  dds_results,
  f_threshold = 99,
  point_size = 3,
  point_color = "gray30",
  point_alpha = 0.5
)

Arguments

dds_fit	A DESeqDataSet object after model fitting.
dds_results	A DESeqResults object derived from dds_fit.
f_threshold	Percentile of the F distribution used as the cutoff for calling outliers.
point_size	Plot point size.
point_color	Plot point color.
point_alpha	Plot point color alpha value.

Details

Obtains the max Cook's distance for a feature across all samples and compares it to the Wald statistic derived from the statistical test for differential expression. Extreme Cook's distance values are truncated to the y-axis upper limit to aid with visualization.

Value

A ggplot object.

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.