getTFtargets {ELMER} | R Documentation |
This function uses ELMER analysis results and summarizes the possible genes targets for each TF
getTFtargets( pairs, enriched.motif, TF.result, dmc.analysis, mae, save = TRUE, dir.out = "./", classification = "family", cores = 1, label = NULL )
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. |
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)