calculateTFactS: calculates TFactS

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

calculates TFactS

Description

This function calculates TFactS

Usage

calculateTFactS(
  DEGs,
  catalog,
  TFs,
  all.targets,
  Q.value = FALSE,
  lambda1 = seq(0.05, 0.5, 0.01),
  lambda2 = 0.05,
  nRep = 100,
  TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME."
)

Arguments

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
Q.value	logical. If it is TRUE, Q.value by Storey method.
lambda1	a vector of the lambda values utilized to obtain pi0.lambda
lambda2	a user-specified threshold of E-value (default: 0.05)
nRep	number of random selections (default: 100)
TF.col	the name of the column that contains the TF names

Value

data.frame

Author(s)

Atsushi Fukushima

References

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

Examples

data(DEGs)
data(catalog)

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

res <- calculateTFactS(DEGs, catalog, TFs, all.targets)

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