calculateRC: calculates Random Control (RC)

In TFactSR: Enrichment Approach to Predict Which Transcription Factors are Regulated

calculates Random Control (RC)

Description

This function calculates Random Control (RC)

Usage

calculateRC(
  df,
  DEGs,
  catalog,
  TFs,
  all.targets,
  TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME.",
  lambda = 0.05,
  nRep = 100
)

Arguments

df	a data frame containng p-values
DEGs	a character vector of DEGs (differentially expressed genes)
catalog	a data frame of TFactS catalog (ver. 2)
TFs	a character vector of transcription factor
all.targets	a character vector of all target genes
TF.col	the name of the column that contains the TF names
lambda	a user-specified threshold of E-value (default: 0.05)
nRep	number of random selections (default: 100)

Value

data.frame

Author(s)

Atsushi Fukushima Definition: m is the number of target genes annotated for the TF under consideration n is the number of query genes N is the number of regulations in the catalog k is the number of query genes that are annotated as regulated by TF (i.e., the intersection between the query and the TF signature)

References

Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.

Examples

data(example.df)
data(catalog)
data(DEGs)

tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs
all.targets <- tftg$all.targets

res <- calculateRC(example.df, DEGs, catalog, TFs, all.targets)

TFactSR documentation built on Aug. 31, 2023, 5:09 p.m.