Update 2 files

- /02_MultiMIR/MultiMiR.R
- /04_Cytoscape/extract_mrna_names_from_mirna.R

02_MultiMIR/MultiMiR.R

-library(readxl)
-library(multiMiR)
-library(writexl)
+# Load required libraries
+library(readxl)    # For reading data from Excel files
+library(multiMiR)  # For querying validated miRNA-mRNA interactions
+library(writexl)   # For writing data to Excel files
 
+# Read data from an Excel file named "miRNAmRNA.xlsx" and store it in the "new_list" variable.
 new_list <- read_excel("miRNAmRNA.xlsx", header = TRUE)
 
+# Get validated miRNA-mRNA interactions using the "multiMiR" package.
+# In this case, the interactions are queried for human (hsa) miRNAs (mirnames) from the "validated" table.
+# The results will be summarized and stored in the "multimir_results" variable.
 multimir_results <- get_multimir(org     = 'hsa',
                                  mirna   = mirnames,
                                  table   = 'validated',
                                  summary = TRUE)
+
+# Display the first few rows of the "multimir_results" data to get an overview of the miRNA-mRNA interactions.
 head(multimir_results@data)
 
+# Extract the results of miRNA-mRNA interactions from the "multimir_results" variable and store them in the "targets" variable.
 targets <- multimir_results@data
+
+# Specify the Excel file name where the results will be saved.
 excel_file <- "multimir_results.xlsx"
-write_xlsx(targets, path = excel_file )
+
\ No newline at end of file
+# Write the "targets" data to an Excel file with the specified file name.
+write_xlsx(targets, path = excel_file)

04_Cytoscape/extract_mrna_names_from_mirna.R

-library(readxl)
-library(multiMiR)
-library(writexl)
+# Load required libraries
+library(readxl)    # For reading data from Excel files
+library(multiMiR)  # For querying validated miRNA-mRNA interactions
+library(writexl)   # For writing data to Excel files
 
+# Read data from an Excel file named "miRNAmRNA.xlsx" and store it in the "new_list" variable.
 new_list <- read_excel("C:/Users/Emre/Desktop/miRNAmRNA.xlsx", header = TRUE)
 
+# Get validated miRNA-mRNA interactions using the "multiMiR" package.
+# In this case, the interactions are queried for human (hsa) miRNAs (mirnames) from the "validated" table.
+# The results will be summarized and stored in the "multimir_results" variable.
 multimir_results <- get_multimir(org     = 'hsa',
                                  mirna   = mirnames,
                                  table   = 'validated',
                                  summary = TRUE)
+
+# Display the first few rows of the "multimir_results" data to get an overview of the miRNA-mRNA interactions.
 head(multimir_results@data)
 
+# Extract the results of miRNA-mRNA interactions from the "multimir_results" variable and store them in the "targets" variable.
 targets <- multimir_results@data
+
+# Specify the Excel file path where the results will be saved.
 excel_file <- "C:/Users/Emre/Desktop/Bioinformatik/Bioinformatik 2.Semester Master/Data Science in the Life Sciences/Project/multimir_results.xlsx"
-write_xlsx(targets, path = excel_file )
 
+# Write the "targets" data to an Excel file with the specified file path.
+write_xlsx(targets, path = excel_file)
 
+# Read data from the "multimir_results_cyto.xlsx" file into the "df" variable.
 df <- read_excel("C:/Users/Emre/Desktop/multimir_results_cyto.xlsx")
+
+# Read data from the "mRNAs.xlsx" file into the "mrna" variable.
 mrna <- read_excel("C:/Users/Emre/Desktop/mRNAs.xlsx")
 
+# Extract the external gene names from the "mrna" data and store them in the "mrna_genes" variable.
 mrna_genes <-  mrna$external_gene_name
 
+# Filter the "df" data based on whether the "target_symbol" column contains gene names present in the "mrna_genes" variable.
 filtered_df <- df[df$target_symbol %in% mrna_genes | duplicated(df$target_symbol) %in% mrna_genes, ]
 
+# Print the filtered data.
 print(filtered_df)
 
-output_file <- ("C:/Users/Emre/Desktop/cytoscape.xlsx")
+# Specify the output Excel file path where the filtered data will be saved.
+output_file <- "C:/Users/Emre/Desktop/cytoscape.xlsx"
+
+# Write the filtered data to an Excel file with the specified file path.
 write_xlsx(filtered_df, output_file)