extract_significant_genes: Extract the sets of genes which are significantly up/down...

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

Extract the sets of genes which are significantly up/down regulated from the combined tables.

Description

Given the output from combine_de_tables(), extract the genes in which we have the greatest likely interest, either because they have the largest fold changes, lowest p-values, fall outside a z-score, or are at the top/bottom of the ranked list.

Usage

extract_significant_genes(
  combined,
  according_to = "all",
  lfc = 1,
  p = 0.05,
  sig_bar = TRUE,
  z = NULL,
  n = NULL,
  min_mean_exprs = NULL,
  exprs_column = NULL,
  top_percent = NULL,
  p_type = "adj",
  invert_barplots = FALSE,
  excel = NULL,
  fc_column = NULL,
  p_column = NULL,
  siglfc_cutoffs = c(0, 1, 2),
  column_suffix = TRUE,
  gmt = FALSE,
  category = "category",
  fancy = FALSE,
  phenotype_name = "phenotype",
  set_name = "set",
  current_id = "ENSEMBL",
  comparison = "orequal",
  required_id = "ENTREZID",
  min_gmt_genes = 10,
  ...
)

Arguments

combined	Output from combine_de_tables().
according_to	What tool(s) decide 'significant?' One may use the deseq, edger, limma, basic, meta, or all.
lfc	Log fold change to define 'significant'.
p	(Adjusted)p-value to define 'significant'.
sig_bar	Add bar plots describing various cutoffs of 'significant'?
z	Z-score to define 'significant'.
n	Take the top/bottom-n genes.
min_mean_exprs	Add a minimum expression value.
exprs_column	Use this column to define expression.
top_percent	Use a percentage to get the top-n genes.
p_type	use an adjusted p-value?
invert_barplots	Invert the significance barplots as per Najib's request?
excel	Write the results to this excel file, or NULL.
fc_column	Column in the DE data containing the foldchange values.
p_column	Column in the DE data containing the pvalues.
siglfc_cutoffs	Set of cutoffs used to define levels of 'significant.'
column_suffix	Used to help determine which columns are used to find significant genes via logfc/p-value.
gmt	Write a gmt file using this result?
category	When writing gmt files, set the category here.
fancy	Write fancy plots with the xlsx file?
phenotype_name	When writing gmt files, set the phenotype flag here.
set_name	When writing gmt files, assign the set here.
current_id	Choose the current ID type for an output gmt file.
comparison	The cutoff may be '>|<' or '<=|>='.
required_id	Choose the desired ID type for an output gmt file.
min_gmt_genes	Define the minimum number of genes in a gene set for writing a gmt file.
...	Arguments passed into arglist.

Value

The set of up-genes, down-genes, and numbers therein.

See Also

combine_de_tables

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