FracFixR (version 1.0.0)

DiffPropTest: DiffPropTest: Statistical Testing for Differential Proportions

Description

Performs statistical testing to identify transcripts with significantly different proportions between conditions in specified fraction(s). Implements three test options: GLM (most powerful), Logit, and Wald.

Usage

DiffPropTest(NormObject, Conditions, Types, Test = c("GLM", "Logit", "Wald"))

Value

Data frame with columns:

• transcript: transcript identifier

• mean_success_cond1/2: mean proportions in each condition

• mean_diff: difference in proportions

• log2FC: log2 fold change

• pval: p-value from statistical test

• padj: FDR-adjusted p-value

Arguments

NormObject

Output from FracFixR() function

Conditions

Character vector of exactly 2 conditions to compare

Types

Character vector of fraction type(s) to analyze. Can be single fraction or multiple (will be combined)

Test

Statistical test to use: "GLM", "Logit", or "Wald"

Details

• GLM: Uses binomial generalized linear model (most statistically powerful)

• Logit: Faster alternative using logit transformation

• Wald: Beta-binomial Wald test for overdispersed count data

Examples

data(example_counts)
data(example_annotation)

# Run FracFixR
results <- FracFixR(example_counts, example_annotation, parallel=FALSE)
# Run differential testing
diff_results <- DiffPropTest(results,
                            Conditions = c("Control", "Treatment"),
                            Types = "Heavy_Polysome",
                            Test = "GLM")