pipe.TranscriptCluster: Hierarchical Clustering of Transcriptomes.

Description Usage Arguments Details Value Author(s)

Description

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

Usage

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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 Dec. 14, 2018, 3:04 p.m.