pipe.TranscriptCluster: Hierarchical Clustering of Transcriptomes.

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Hierarchical Clustering of Transcriptomes.

Description

Combine a set of sample transcriptomes into a matrix and pass it to the hierarchical clustering tool.

Usage

pipe.TranscriptCluster(sampleIDset = NULL, annotationFile = "Annotation.txt", 
		optionsFile = "Options.txt", results.path = NULL, speciesID = getCurrentSpecies(), 
		intensityColumn = "RPKM_M", useLog = FALSE, label = "")

Arguments

sampleIDset	The set of SampleIDs to compare by clustering.
annotationFile	File of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.
optionsFile	File of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
speciesID	The SpeciesID of the target species to calculate a transcriptome for. By default, transcriptome for all species in the current target are generated.
results.path	The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.
intensityColumn	Character string of one column name in the standard transcriptome files.
useLog	Logical, should the intensity values be log transformed prior to clustering.
label	Character string passed to the plot routine, added to the main header.

Details

A simple wrapper function that first builds a matrix of gene expression, by calling expressionFileSetToMatrix, and then passing that on the the clustering tool expressionCluster.

Value

Invisibly, a list with 2 elements:

expressionMatrix	a data frame of gene expression, with columns for GeneID, Product, and then a column of intensity values for each sample.
cluster	the results object passed back from the clustering tool.

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.