combine_single_de_table: Given a limma, edger, and deseq table, combine them into one.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Given a limma, edger, and deseq table, combine them into one.

Description

This combines the outputs from the various differential expression tools and formalizes some column names to make them a little more consistent.

Usage

combine_single_de_table(
  li = NULL,
  ed = NULL,
  eb = NULL,
  de = NULL,
  ba = NULL,
  table_name = "",
  final_table_names = c(),
  wanted_numerator = NULL,
  wanted_denominator = NULL,
  invert_table = FALSE,
  invert_plots = FALSE,
  annot_df = NULL,
  adjp = TRUE,
  padj_type = "fdr",
  include_deseq = TRUE,
  include_edger = TRUE,
  include_ebseq = TRUE,
  include_limma = TRUE,
  include_basic = TRUE,
  lfc_cutoff = 1,
  p_cutoff = 0.05,
  format_sig = 4,
  do_inverse = FALSE,
  excludes = NULL,
  sheet_count = 0
)

Arguments

li	Limma output table.
ed	Edger output table.
eb	EBSeq output table
de	DESeq2 output table.
ba	Basic output table.
table_name	Name of the table to merge.
final_table_names	Vector of the final table names.
wanted_numerator	The numerator we would like to find.
wanted_denominator	The denominator we would like to find.
invert_table	Boolean to see if we already think we should switch n/d
invert_plots	Conversely, we can invert the plots.
annot_df	Add some annotation information?
adjp	Use adjusted p-values?
padj_type	Add this consistent p-adjustment.
include_deseq	Include tables from deseq?
include_edger	Include tables from edger?
include_ebseq	Include tables from ebseq?
include_limma	Include tables from limma?
include_basic	Include the basic table?
lfc_cutoff	Preferred logfoldchange cutoff.
p_cutoff	Preferred pvalue cutoff.
format_sig	How many significant digits to print? Set it to something not numeric to not use any significant digit formatting.
do_inverse	Dead parameter? invert the data?
excludes	Set of genes to exclude from the output.
sheet_count	What sheet is being written?

Value

List containing a) Dataframe containing the merged limma/edger/deseq/basic tables, and b) A summary of how many genes were observed as up/down by output table.

See Also

[data.table] [hpgl_padjust()] [extract_keepers_all()] [extract_keepers_lst()] [extract_keepers_single()]

elsayed-lab/hpgltools documentation built on April 8, 2024, 1:30 a.m.