simple_dorothea: Invoke dorothea in an attempt to hunt down cool TFs.

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

Invoke dorothea in an attempt to hunt down cool TFs.

Description

dorothea: https://github.com/saezlab/dorothea appears to provide experimentally verified mappings from genes->transcription factors as well as a set of functions which allow one to pass it an expressionset/matrix of counts(log scale) and get back scores by tf. This function is an attempt to smooth it out and prod it for usability.

Usage

simple_dorothea(
  expt,
  gene_column = "ensembl_gene_id",
  hgnc_column = "hgnc_symbol",
  transform = "log2",
  conf = c("A", "B", "C"),
  dorothea_options = NULL,
  lfc = 1,
  p = 0.05,
  species = "hsapiens"
)

Arguments

expt	Expressionset
gene_column	Column in fData containing the gene IDs.
hgnc_column	fData column containing the HGNC symbols as used by dorothea/viper
transform	Explicitly set the scale to log2 (TODO: improve this)
conf	Vector of confidence scores to filter the data.
dorothea_options	Optional configuration list.
lfc	Fold-change cutoff.
p	P-value cutoff.
species	Either human or mouse.

Value

list containing some information from dorothea and limma.

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