combine_mapped_table: Combine data taken from map_keepers() into a single large...
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

combine_mapped_table

R Documentation

Combine data taken from map_keepers() into a single large table.

Description

This is part of an ongoing attempt to simplify and clean up the combine_de_tables() function. I am hoping that map_keepers and this will be able to take over all the logic currently held in the various extract_keepers_xxx() functions.

Usage

combine_mapped_table(
  entry,
  includes,
  adjp = TRUE,
  padj_type = "fdr",
  annot_df = NULL,
  excludes = NULL,
  lfc_cutoff = 1,
  p_cutoff = 0.05,
  format_sig = 4,
  sheet_count = 0
)

Arguments

`entry`	Single entry from map_keepers() which provides orientation information about the table from all_pairwise(), along with the actual data.
`includes`	List of methods to include.
`adjp`	Used adjusted pvalues when defining 'significant.?
`padj_type`	Perform this type of pvalue adjustment.
`annot_df`	Include these annotations in the result tables.
`excludes`	When provided, exclude these genes.
`lfc_cutoff`	Use this value for a log2FC significance cutoff.
`p_cutoff`	Use this value for a(n adjusted) pvalue significance cutoff.
`format_sig`	Use this many significant digits for some of the unwieldy numbers.
`sheet_count`	Start with these sheet number and increment for excel.