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

In 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,
                      title = NULL, 
                      width = 10, 
                      height = NULL,
                      summary = FALSE)

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 specify 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 outputs figure.
title	Plot title. Default: no title
width	Plot width
height	Plot height. If NULL a default value will be calculated
summary	Create a summary table along with the plot, it is necessary to add two new columns to object (NumOfProbes and PercentageOfProbes)

Details

motif.enrichment If input data.frame object, it should contain "motif", "OR", "lowerOR", "upperOR" columns. motif specifies name of motif; OR specifies Odds Ratio, lowerOR specifies lower boundary of OR (95 upperOR specifies upper boundary of OR(95

significant A list used to select subset of motif.enrichment by the cutoff of OR, lowerOR, upperOR. significant=list(OR=1). More than one cutoff can be specified such as significant = list(OR=1, lowerOR=1,upperOR=4)

Value

A figure shows the enrichment level for selected motifs.

Author(s)

Lijing Yao (creator: [e-mail])

References

Yao, Lijing, et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome biology 16.1 (2015): 1.

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(10,3,1.09,1.9,1.5,1.9, 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)
motif.enrichment.plot(motif.enrichment = motif.enrichment,
                      significant = list(OR = 3),
                      label = "hypo", 
                      title = "OR for paired probes hypomethylated in Mutant vs WT",
                      save = FALSE)
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),
                               NumOfProbes = c(23,5,3,7,6,5,5),
                               PercentageOfProbes = c(0.23,0.05,0.03,0.07,0.06,0.05,0.05),
                               stringsAsFactors=FALSE)
motif.enrichment.plot(motif.enrichment = motif.enrichment,
                      significant = list(OR = 3),
                      label = "hypo", save = FALSE)
motif.enrichment.plot(motif.enrichment = motif.enrichment,
                      significant = list(OR = 3),
                      label = "hypo", 
                      summary = TRUE,
                      title = "OR for paired probes hypomethylated in Mutant vs WT",
                      save = TRUE)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.