schematic.plot: schematic.plot to plot schematic plots showing the locations...

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

Description

schematic.plot is a function to plot schematic plots showing the locations of genes and probes.

Usage

schematic.plot(pair, byProbe, byGene, byCoordinate = list(chr = c(), start =
  c(), end = c()), dir.out = "./", save = TRUE, ...)

Arguments

pair	A Pair object. All slots of Pair class should be included
byProbe	A vector of probe names.
byGene	A vector of gene ID
byCoordinate	A list contains chr, start and end. byCoordinate=list(chr=c(),start=c(),end=c()).
dir.out	A path specifies the directory for outputs. Default is current directory
save	A logic. If true, figures will be saved to dir.out.
...	Parameters for GetNearGenes function. See GetNearGenes

Details

byProbes: When a vector of probes' name are provided, function will produce schematic plots for each individual probes. The schematic plot contains probe, nearby 20 (or the number of gene user specified.) genes and the significantly linked gene to the probe.

byGene: When a vector of gene ID are provided, function will produce schematic plots for each individual genes. The schematic plot contains the gene and all the significantly linked probes.

byCoordinate: When a genomic coordinate is provided, function will produce a schematic plot for this coordinate. The schematic plot contains all genes and significantly linked probes in the range and the significant links.

Value

Schematic plots will be produced.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

library(grid)
load(system.file("extdata","mee.example.rda",package = "ELMER"))
nearGenes <-GetNearGenes(TRange=getProbeInfo(mee,probe=c("cg00329272","cg19403323")),
                        geneAnnot=getGeneInfo(mee))
Hypo.pair <-get.pair(mee=mee,probes=c("cg00329272","cg19403323"),
                    nearGenes=nearGenes,permu.size=5,Pe = 0.2,dir.out="./",
                    label= "hypo")
pair <- fetch.pair(pair=Hypo.pair,
                  probeInfo = getProbeInfo(mee),
                  geneInfo = getGeneInfo(mee))
# a. generate schematic plot of one probe with nearby 20 genes and label
#the gene significantly linked with the probe.
grid.newpage()
schematic.plot(pair=pair, byProbe="cg19403323" ,save=FALSE)
#b. generate schematic plot of ont gene with the probe which the gene significanlty linked to.
grid.newpage()
schematic.plot(pair=pair, byGene="ID255928",save=FALSE)

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