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

View source: R/de_xlsx.R

combine_single_de_tableR Documentation

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 May 9, 2024, 5:02 a.m.