Hi LChart

In the code, what is the input file here. It's getting more confusion now. Can you help me provide a code in R( as I am using metap package for fisher'method).

I used this code in R:

library(readr)
p_values_list <- list()
gene_ids_list <- list()
csv_file_names <- list()
csv_files <- c("file1.csv", "file2.csv", "file3.csv")
for (file in csv_files) {
data <- read_csv(file, col_types = cols_only(geneID = col_character(), pvalue = col_double(), log2FoldChange = col_double()))
if ("pvalue" %in% colnames(data) && "geneID" %in% colnames(data) && "log2FoldChange" %in% colnames(data)) {
p_values <- data[!is.na(data$pvalue), "pvalue"]
gene_ids <- data[!is.na(data$pvalue), "geneID"]
p_values_list[[file]] <- p_values
gene_ids_list[[file]] <- gene_ids
csv_file_names[[file]] <- file
} else {
warning("Missing or incorrect column names in ", file)
}
}
combined_p_values <- -2 * sum(log(na.omit(unlist(p_values_list))))
meta_p_value <- 1 - pchisq(combined_p_values, df = 2 * length(unlist(p_values_list)))
significance_threshold <- 0.05
metaDEGs <- unlist(gene_ids_list)[meta_p_value < significance_threshold]
metaDEGs_csv <- rep(csv_files, length.out = length(metaDEGs))
result <- data.frame(GeneID = metaDEGs, CSV_File = metaDEGs_csv)
print(result)

The output was:

GeneID  CSV_File    
file1.csv.geneID1   CmV2_2M004200   file1.csv
file1.csv.geneID2   CmV2_1M008990   file2.csv
file1.csv.geneID3   CmV2_6M054550   file3.csv

You can see here. the output was a mess, giving wrong information about csv file to which particular genes expressed belongs. Also, I need information about the direction of which expressed genes (whether they un-regulated or downregulated), which is missing here.

So, I really need some help here!!!