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

In 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(data,
               group.col = NULL,
               group1 = NULL,
               group2 = NULL,
               pair,
               byProbe,
               byGeneID,
               byCoordinate=list(chr=c(), start=c(), end=c()),
               statehub.tracks,
               dir.out="./",
               save=TRUE,...)

Arguments

data	A Multi Assay Experiment object with DNA methylation and gene expression Summarized Experiment objects
group.col	A column defining the groups of the sample. You can view the available columns using: colnames(MultiAssayExperiment::colData(data)).
group1	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
group2	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.#' @param byProbe A vector of probe names.
pair	A data frame with three columns: Probe, Gene ID (Ensemble gene ID) and Pe (empirical p-value). This is the ouput of get.pair function.
byProbe	A vector of probe names
byGeneID	A vector of gene ID
byCoordinate	A list contains chr, start and end. byCoordinate=list(chr=c(),start=c(),end=c()).
statehub.tracks	Relative path to a statehub track.
dir.out	A path specify the directory for outputs. Default is current directory
save	A logic. If true, figures will be saved to dir.out.
...	Parameters for 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.

Examples

data <- ELMER:::getdata("elmer.data.example")
pair <- data.frame(Probe = c("cg19403323","cg19403323", "cg26403223"),
                   GeneID = c("ENSG00000196878", "ENSG00000009790", "ENSG00000009790" ),
                   Symbol = c("TRAF3IP3","LAMB3","LAMB3"),
                   Raw.p =c(0.001,0.00001,0.001),
                   Pe = c(0.001,0.00001,0.001))
schematic.plot(data,
               group.col = "definition",
               group1 = "Primary solid Tumor",
               group2 = "Solid Tissue Normal",
               pair = pair,
               byProbe = "cg19403323")
schematic.plot(data,
               group.col = "definition",
               group1 = "Primary solid Tumor",
               group2 = "Solid Tissue Normal",
               pair = pair,
               byGeneID = "ENSG00000009790")

schematic.plot(data,
               group.col = "definition",
               group1 = "Primary solid Tumor",
               group2 = "Solid Tissue Normal",
               pair = pair,
               byCoordinate = list(chr="chr1", start = 209000000, end = 209960000))
## Not run: 
   schematic.plot(data,
                  group.col = "definition",
                  group1 = "Primary solid Tumor",
                  group2 = "Solid Tissue Normal",
                  pair = pair,
                  byProbe = "cg19403323",
                  statehub.tracks = "hg38/ENCODE/mcf-7.16mark.segmentation.bed")

## End(Not run)

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