FASTcalculateRC {TFactSR}

calculates Random Control (RC) fastly?

Description

This function calculates Random Control (RC)

Usage

FASTcalculateRC(
  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

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