Converts DESeq2 results object to MetaVolcanoR format with confidence intervals
prepare_deseq2(deseq_result, gene_column = "GeneID")
Arguments
- deseq_result
A DESeq2 results object from results() or lfcShrink()
- gene_column
Character string specifying which column to use as gene
identifier. Default is "GeneID" (rownames). Can also be a column name
if gene symbols are in the rowData.
Value
A data.frame with columns: Symbol, Log2FC, pvalue, CI.L, CI.R
Examples
if (FALSE) { # \dontrun{
library(DESeq2)
dds <- DESeqDataSet(se, design = ~ condition)
dds <- DESeq(dds)
res <- results(dds)
# Prepare for MetaVolcanoR
deg_table <- prepare_deseq2(res)
# Use in meta-analysis
meta_result <- rem_mv(list(study1 = deg_table, study2 = deg_table2))
} # }