densityplotAll_oligo: Density plots for microarrays

In machalen/QualityGraphsOligo: Make quality graphs for microarray data based on objects obtained with oligo normalization.

Description

This function makes density plots from the GeneFeatureSet object generated with oligo package.

Usage

densityplotAll_oligo(ds, labels, picname, groupn = NULL, all = FALSE, resDir = NULL)

Arguments

ds	GeneFeatureSet object obtained with: RawData <- read.celfiles(celFiles.s, sampleNames= celnames.s)
labels	Optional. Vector with sample names. Samples are in the same order as in the ds object. Default get sample names from the ds object.
picname	Name of output files.
groupn	Optional. Number of samples to include in each density plot. If the number is lower than total number of samples, more than one plot is going to be shown. Default is groupn = all samples.
all	Optional. If TRUE, an additional plot with all density plots made with a groupn is made.
resDir	Output directory. Default is resultsDir.

Details

This function outputs density plots from a GeneFeatureSet object obtained with oligo package and the function read.celfiles(). Plots are made using the log2 transformation of the intensity signal. If a large amount of samples is contained in the ds object, it could be dificult to distinguish one from another. Using the additional parameter groupn, a lower number of samples can be defined to be ploted. For example if there are 24 samples in the ds object, seting groupn=12, two plots of 12 samples each will be made. If all=TRUE, all plots generated by the function will be shown in the same plot.

Value

Output is a .png file with the index of the arrays in the title in resDir.

Author(s)

Magdalena Arnal Segura <[e-mail]>

machalen/QualityGraphsOligo documentation built on May 28, 2019, 2:32 a.m.