motif.enrichment.plot: motif.enrichment.plot to plot bar plots showing motif...

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs. Option motif.enrichment can be a data frame generated by get.enriched.motif or a path of XX.csv saved by the same function.

Usage

motif.enrichment.plot(motif.enrichment, significant = NULL, dir.out = "./",
  save = TRUE, label = NULL)

Arguments

motif.enrichment	A data frame or a file path of get.enriched.motif output motif.enrichment.csv file.
significant	A list to select subset of motif. Default is NULL.
dir.out	A path specifies the directory to which the figures will be saved. Current directory is default.
save	A logic. If true (default), figure will be saved to dir.out.
label	A character labels the output figures.

Value

A figure shows the enrichment level for selected motifs.

Author(s)

Lijing Yao (maintainer: [e-mail])

References

Yao L, Shen H, Laird PW, Farnham PJ,Berman BP: Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes. in revision of Genome Biology

Examples

motif.enrichment <- data.frame(motif=c("TP53","NR3C1","E2F1","EBF1","RFX5",
"ZNF143", "CTCF"),
OR=c(19.33,4.83,1, 4.18, 3.67,3.03,2.49),
lowerOR =c(10,3,1.09,1.9,1.5,1.5, 0.82),
upperOR =c(23,5,3,7,6,5,5),
stringsAsFactors=FALSE)
motif.enrichment.plot(motif.enrichment=motif.enrichment,
                     significant=list(OR=3),
                     label="hypo", save=FALSE)

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.