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Funnel plot for one gene

Source: R/07_visualize.R
mx_funnel.Rd

Plots each study's log2 fold change against its standard error, with the pooled estimate and pseudo 95% confidence limits. Asymmetry suggests small-study effects; see mx_small_study for formal tests.

Usage

mx_funnel(gene, de_results, meta_result = NULL)

Arguments

gene

Gene identifier.

de_results

Named list of per-study DE data.frames or metaXpressStudy objects.

meta_result

Optional metaXpressResult; its pooled estimate is used as the funnel centre. Otherwise the inverse-variance fixed-effect estimate is used.

Value

A ggplot2 object.

References

Sterne, J.A.C. & Egger, M. (2001) Funnel plots for detecting bias in meta-analysis: guidelines on choice of axis. Journal of Clinical Epidemiology, 54(10), 1046–1055. doi:10.1016/S0895-4356(01)00377-8

See also

mx_small_study, mx_forest

Examples

ad <- readRDS(system.file("extdata", "ad_brain_de.rds",
                          package = "metaXpress"))
mx_funnel("GFAP", ad$de_results)