Nothing
## ---- echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE--------------------
library(ELMER.data)
library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)
## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"--------------
# Load results from previous sections
mae <- get(load("mae.rda"))
load("result/getMotif.hypo.enriched.motifs.rda")
## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"--------------
## identify regulatory TF for the enriched motifs
TF <- get.TFs(data = mae,
group.col = "definition",
group1 = "Primary solid Tumor",
group2 = "Solid Tissue Normal",
mode = "unsupervised",
enriched.motif = enriched.motif,
dir.out = "result",
cores = 1,
label = "hypo")
## ----eval=TRUE, message=FALSE, warning = FALSE--------------------------------
# get.TFs automatically save output files.
# getTF.hypo.TFs.with.motif.pvalue.rda contains statistics for all TF with average
# DNA methylation at sites with the enriched motif.
# getTF.hypo.significant.TFs.with.motif.summary.csv contains only the significant probes.
dir(path = "result", pattern = "getTF")
# TF ranking plot based on statistics will be automatically generated.
dir(path = "result/TFrankPlot/", pattern = "pdf")
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