create_DEresults: Title

In IMBEIbioinformatics/BIUMmisc: A collection of functions and scripts commonly used by the BIUM-MZ Core Facility and the Bioinformatics group at the IMBEI

Title

Description

Title

Usage

create_DEresults(
  resuSet = NULL,
  dds_obj,
  contrast_name,
  FDR = 0.05,
  lfc_threshold = 0,
  extended_anno_df,
  species = "Homo_sapiens",
  name_res_entry = contrast_name,
  verbose = TRUE
)

Arguments

resuSet	A list, provided in the format expected by the resuSet specifications. This can be an empty list, if the object was never created beforehand, otherwise this function can simply add all the set of the results and output into a new element of an existing list. Defaults to NULL, which would lead to the creation of a new list object. If this is not the desired behavior, please provide an existing object structured as a resuSet.
dds_obj	A DESeqDataset object, meaningfully related/matched to the resuSet object.
contrast_name	Character string, specifying the name of the contrast to be extracted
FDR	Numeric value, specifying the false discovery rate value to be used
lfc_threshold	Numeric value, corresponding to the logFC theshold to be used to extract the results - it is relevant in the call to results() and it does differ (a lot, conceptually) from the logFC filtering that commonly is performed post-hoc, after testing against the default null hypothesis (logFC = 0), which might be too liberal in some cases.
extended_anno_df	An annotation data.frame with the following columns: gene_id and gene_name (mandatory), and description (optional, can be retrieved via biomaRt)
species	Character string, specifying the species for the dataset under investigation. Defaults to "Homo_sapiens", could also be "Mus_musculus" and other similarly assembled character strings. This is relevant only when creating the buttons for the interactive versions of the results tables.
name_res_entry	Character string
verbose	Logical

Value

A resuSet list object.

Examples

# TODO

IMBEIbioinformatics/BIUMmisc documentation built on June 12, 2025, 10:50 p.m.