layoutEpigeneticEV: Create a layout dataset format for plotting and better data...

Description Usage Arguments Value Examples

View source: R/epiGPlotFunctions.R

Description

Cleans up the parsed csv/rda file data from obtained dataset, and returns a layout that can be used for plotting

Usage

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layoutEpigeneticEV(
  dataFrame,
  normalized = FALSE,
  sample.class = c(),
  class.colour = c()
)

Arguments

dataFrame

The n x 4 data frame loaded from csv/rda using the functions above

normalized

Whether or not to perform normalization on expression values

sample.class

Chooses and subset a specific sample class from the data frame and use it for layout

class.colour

User can specify a list/vector custom colour palette of length equals to number of given sample classes

Value

Returns a layout containing 4 columns of: expression value, quantile over all genes, colour, sample class with their row names assigned as their sample genes

Examples

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## Not run: 
rawData <- EpiGPlot::loadEpigeneticData("data/NO66_HUMAN.rda")
gLayout <- EpiGPlot::layoutEpigeneticEV(rawData,
                                       sample.class=c("cell_line", "tissue"),
                                       class.colour=c("red", "blue"))
nrow(gLayout) # 390
unique(gLayout$Colour) # "red", "blue"

## End(Not run)

kevbobli224/EpiGPlot documentation built on Dec. 21, 2021, 6:35 a.m.