% 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"
)

}