Analyze Gene Expression Between Groups

Performs a comprehensive statistical analysis comparing gene expression between two groups. Integrates parametric and nonparametric testing, effect size estimation, bootstrapped confidence intervals, and a heuristic biological relevance assessment.

Usage

analyze.gene(df, alpha = 0.05, n.boot = 1000)

Arguments

df

A data frame as produced by build.analysis.df(), containing at least two columns:

expression

Numeric vector of gene expression values.

group

Character or factor vector with exactly two group labels.

When the data frame contains multiple genes (i.e., a gene column with more than one unique value), expression values from all genes are pooled together. Subset the data frame to a single gene before calling this function for per-gene results.

alpha

Numeric. Significance threshold. Default is 0.05.

n.boot

Integer. Number of bootstrap resamples for the confidence interval. Default is 1000.

Value

A named list with nine elements:

p.value

Numeric. P-value from the adaptive t-test.

effect.size

Numeric. Cohen's d.

effect.size.class

Character. Qualitative magnitude label from classify.effect.size().

confidence.interval

Named list with lower and upper bounds for the bootstrapped CI around Cohen's d.

nonparametric.p

Numeric. P-value from the Wilcoxon rank-sum test.

robustness

Character. Agreement assessment between parametric and nonparametric tests.

biological.relevance

Character. Heuristic relevance label from flag.biological.relevance().

interpretation

Character. Human-readable summary combining all of the above.

raw

List. Raw output from the parametric and nonparametric tests for further inspection.

Details

This function integrates multiple statistical perspectives to provide a more complete picture of group differences than a p-value alone. The result is designed to feed directly into plot.gene.analysis() for visualization.

Examples

# \donttest{
geo <- extract.expression(load.geo.soft(accession = "GDS3268", log.transform = TRUE))
#> GDS3268 not found locally, downloading from NCBI GEO...
#> Warning: NaNs produced
probe <- find.probe.by.gene(geo$gene, "mucin 20, cell surface associated")
expr <- get.gene.expression(geo$expression, probe)
analysis.df <- build.analysis.df(expr, geo$phenotype, geo$gene)
result <- analyze.gene(analysis.df, n.boot=100)
cat(result$interpretation)
#> The difference is not statistically significant with a negligible effect size.
#> Result is no consistent evidence of difference.
#> No strong evidence of biological relevance.
# }