Prepare limma results for MetaVolcanoR — prepare

Converts limma topTable results to MetaVolcanoR format

prepare_limma(
  limma_result,
  gene_column = "GeneID",
  fc_column = "logFC",
  pval_column = "P.Value",
  se_column = NULL,
  ci_left = "CI.L",
  ci_right = "CI.R"
)

Arguments

limma_result: A data.frame from limma::topTable()
gene_column: Column name containing gene identifiers (default: "GeneID")
fc_column: Column name containing log fold changes (default: "logFC")
pval_column: Column name containing p-values (default: "P.Value")
se_column: Column name containing standard errors. If NULL, will try to calculate from CI columns or t-statistic
ci_left: Column name for left CI limit (default: "CI.L")
ci_right: Column name for right CI limit (default: "CI.R")

Value

A data.frame with columns: Symbol, Log2FC, pvalue, CI.L, CI.R

Examples

if (FALSE) { # \dontrun{
library(limma)
fit <- lmFit(eset, design)
fit <- eBayes(fit)
top <- topTable(fit, number = Inf)

# Prepare for MetaVolcanoR
deg_table <- prepare_limma(top)
} # }