extract_keepers: When a list of 'keeper' contrasts is specified, extract it...

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

When a list of 'keeper' contrasts is specified, extract it from the data.

Description

This is the most interesting of the extract_keeper functions. It must check that the numerators and denominators match the desired contrast and flip the signs in the logFCs when appropriate.

Usage

extract_keepers(
  extracted,
  keepers,
  table_names,
  all_coefficients,
  apr,
  adjp,
  annot_df,
  includes,
  excludes,
  padj_type,
  fancy = FALSE,
  loess = FALSE,
  lfc_cutoff = 1,
  p_cutoff = 0.05,
  format_sig = 4,
  plot_colors = plot_colors,
  z = 1.5,
  alpha = 0.4,
  z_lines = FALSE,
  label = 10,
  label_column = "hgncsymbol"
)

## S4 method for signature 'list,character'
extract_keepers(
  extracted,
  keepers,
  table_names,
  all_coefficients,
  apr,
  adjp,
  annot_df,
  includes,
  excludes,
  padj_type,
  fancy = FALSE,
  loess = FALSE,
  lfc_cutoff = 1,
  p_cutoff = 0.05,
  format_sig = 4,
  plot_colors = plot_colors,
  z = 1.5,
  alpha = 0.4,
  z_lines = FALSE,
  label = 10,
  label_column = "hgncsymbol"
)

Arguments

extracted	Tables extracted from the all_pairwise data.
keepers	In this case, one may assume either NULL or 'all'.
table_names	The set of tables produced by all_pairwise().
all_coefficients	The set of all experimental conditions in the experimental metadata.
apr	The result from all_pairwise(), containing the limma/edger/deseq/etc data.
adjp	Pull out the adjusted p-values from the data?
annot_df	What annotations should be added to the table?
includes	List of predicates by method.
excludes	Set of genes to exclude.
padj_type	Choose a specific p adjustment.
fancy	Include larger pdf/svg plots with the xlsx output?
loess	Add a loess to plots?
lfc_cutoff	Passed for volcano/MA plots and defining 'significant'
p_cutoff	Passed for volcano/MA plots and defining 'significant'
format_sig	Number of significant digits for stuff like pvalues.
plot_colors	Define what colors should be used for 'up'/'down'
z	Define significantly away from the identity line in a coefficient plot.
alpha	Use this alpha transparency for plots.
z_lines	Include lines denoting significant z-scores?
label	When not NULL, label this many genes.
label_column	Try using this column for labeling genes.

Value

The extracted, but with more stuff at the end!

Methods (by class)

• extract_keepers(extracted = list, keepers = character): Use a character vector instead of a list.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.