--- a
+++ b/man/compare_merge.Rd
@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CompareMerge.R
+\name{compare_merge}
+\alias{compare_merge}
+\title{Compare and merge specific columns from two DEG data frames}
+\usage{
+compare_merge(df1, df2, by_gene, compare_col, suffixes, df_name)
+}
+\arguments{
+\item{df1}{First data frame.}
+
+\item{df2}{Second data frame.}
+
+\item{by_gene}{Column name by which to join the data frames, typically "Gene".}
+
+\item{compare_col}{Column to compare for identity, which will also be the name of the merged column.}
+
+\item{suffixes}{Suffixes to use for non-identical column names in the joined data frame.}
+
+\item{df_name}{Name to assign to the resulting data frame for identification.}
+}
+\value{
+A data frame with processed columns.
+}
+\description{
+This function takes two DEG data frames, inner joins them by a specified gene column,
+checks if a specified column is identical across both data frames, and merges them if they are.
+The resulting data frame will have a merged column named after the compared column.
+}
+\examples{
+# Create simulated DESeq2 data
+DEG_deseq2 <- data.frame(
+  Gene = c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5"),
+  change = c("up", "down", "no_change", "up", "down"),
+  log2FoldChange = c(2.5, -3.2, 0.1, 1.8, -2.5),
+  pvalue = c(0.01, 0.05, 0.9, 0.02, 0.03)
+)
+
+# Display the first 5 rows of the DESeq2 data
+head(DEG_deseq2, 5)
+
+# Create simulated edgeR data
+DEG_edgeR <- data.frame(
+  Gene = c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5"),
+  change = c("up", "down", "no_change", "no_change", "up"),
+  log2FoldChange = c(2.3, -3.1, 0.2, 0.1, 2.7),
+  pvalue = c(0.02, 0.04, 0.8, 0.6, 0.01)
+)
+
+# Display the first 5 rows of the edgeR data
+head(DEG_edgeR, 5)
+
+# Merge the DESeq2 and edgeR data
+deseq2_edgeR <- compare_merge(
+  df1 = DEG_deseq2,
+  df2 = DEG_edgeR,
+  by_gene = "Gene",
+  compare_col = "change",
+  suffixes = c("_1", "_2"),
+  df_name = "deseq2_edgeR"
+)
+
+}