normplots2File: normplots2File

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

normplots2File plots the result of the normalized data and creates a file.

Usage

normplots2File(my.data, sampleNames, my.colors, my.groups,
  my.method = "average", my.cex = 0.7, posText = 4, dim3 = FALSE,
  fileName, outputDir, PCAPlots = TRUE, csv, lFile = NULL)

Arguments

my.data	Normalized data.
sampleNames	Names of the samples of the normalized data.
my.colors	Colores used in the plots.
my.groups	Name of the groups in the plots
my.method	Method used to make the clusters.
my.cex	Cex used in the plots.
posText	Position of the text.
dim3	If TRUE the PCA plot is in 3D.
fileName	Name of the file created.
outputDir	Path of the file created.
PCAPlots	If TRUE PCA plots will be created.
csv	Indicates the file type.
lFile	Name of the links file.

Examples

## Not run: 
load("./ResultsDir/normalizedData.Rda")
repes <- duplicated(exprs(my.norm), MARGIN=1)
exprs(my.norm) <- exprs(my.norm)[!repes,]
eset_norm <- my.norm
my.colors <- rainbow(length(sampleNames(eset_norm)))
my.names <- pData(eset_norm)$ShortName
myCex<- 0.8
dim3 <- FALSE
fileName <- "NormalizedPlots.pdf"
outputDir <- "./ResultsDir"
PCAPlots <- TRUE
csv <- "csv2"
normplots2File(my.data = eset_norm, sampleNames = my.names, my.colors = my.colors,
my.groups = pData(eset_norm)$Group, my.method = "average",my.cex = myCex ,
posText = 2, dim3 = FALSE,fileName = fileName, outputDir = outputDir,PCAPlots = TRUE,
csv = fileType)
## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.