getTFtargets: Get TF target genes

Description Usage Arguments Examples

View source: R/Main_function.R

Description

This function uses ELMER analysis results and summarizes the possible genes targets for each TF

Usage

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getTFtargets(pairs, enriched.motif, TF.result, dmc.analysis, mae,
  save = TRUE, dir.out = "./", classification = "family",
  cores = 1, label = NULL)

Arguments

pairs

Output of get.pairs function: dataframe or file path

enriched.motif

List of probes for each enriched motif: list of file path. The file created by ELMER is getMotif...enriched.motifs.rda

TF.result

Output get.TF function: dataframe or file path

dmc.analysis

DMC results file or data frame

mae

A multiAssayExperiment outputed from createMAE function

save

A logic. If save is true, a files will be saved: getTFtarget.XX..csv If save is false, only a data frame contains the same content with the first file.

dir.out

A path specifies the directory for outputs of get.pair function. Default is current directory

classification

use family or subfamily classification to consider potential TF

cores

Number of cores to be used in parallel

label

A character labels the outputs.

Examples

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pairs <- data.frame(Probe = c("cg26992600","cg26992800","cg26992900"),
                    Symbol = c("KEAP1","DSP","ATP86"))
enriched.motif <- list("FOXD3_HUMAN.H11MO.0.D"= c("cg26992800","cg26992900"))
TF.result <- data.frame(motif = c("FOXD3_HUMAN.H11MO.0.D"),
                        potential.TF.family = c("TP63;TP73"))
getTFtargets(pairs,enriched.motif,TF.result)
 
## Not run: 
getTFtargets("../LUAD_LUSC_analysis_hg38/hyper/getPair.hyper.pairs.significant.csv",
enriched.motif = "../LUAD_analysis_hg38/hyper/getMotif.hyper.enriched.motifs.rda",
TF.result = "../LUAD_analysis_hg38/hyper/getTF.hyper.significant.TFs.with.motif.summary.csv")

## End(Not run)

ELMER documentation built on Nov. 1, 2018, 2:13 a.m.