compare_merge: Compare and merge specific columns from two DEG data frames

In TransProR: Analysis and Visualization of Multi-Omics Data

Compare and merge specific columns from two DEG data frames

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.

Usage

compare_merge(df1, df2, by_gene, compare_col, suffixes, df_name)

Arguments

df1	First data frame.
df2	Second data frame.
by_gene	Column name by which to join the data frames, typically "Gene".
compare_col	Column to compare for identity, which will also be the name of the merged column.
suffixes	Suffixes to use for non-identical column names in the joined data frame.
df_name	Name to assign to the resulting data frame for identification.

Value

A data frame with processed columns.

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"
)

TransProR documentation built on April 4, 2025, 3:16 a.m.