Formatting differential expression results from DESEQ2

Formatting differential expression results from DESEQ2

format_res_deseq(
  dt,
  log2FoldChange = 0,
  padj = 0.05,
  n_label = 10,
  gene_id_conversion = NULL,
  filter_protein_coding = TRUE
)

Arguments

dt

Differential expression results dataframe from DESEQ2

log2FoldChange

Log2FC absolute threshold

padj

adjusted p value threshold. Default to 0.05

n_label

maximum number of label on volcano plot

gene_id_conversion

Default to NULL. Can provide a dataframe with gene_name and uniprot_id columns to easily convert nomenclature.

filter_protein_coding

Logical as whether to filter protein coding gene. Default to TRUE.

Value

Formatted data frame

See also

Other Helper: counts_rna(), format_res_limma(), get_background(), get_metadata(), processed_proteomics(), processed_rna()