Class DEMIExperiment

Description

The class DEMIExperiment defines an experiment. It holds the raw and normalized expression data as well as annotation information for selected analysis (either 'gene', 'transcript', 'exon' or 'genome'). It can be used to hold all the analysis results (DEMIDiff objects) done on the same DEMIExperiment object.

Arguments

analysis

A character. Defines the analysis type. It can be either 'transcript', 'gene', 'exon' or 'genome'. The default value is 'transcript'. For 'genome' analysis sectionsize parameter needs to be defined as well.

celpath

A character. It can point to the directory containing the CEL files or is a vector that points directly to the CEL files.

experiment

A character. A custom name of the experiment defined by the user (e.g. 'myexperiment').

organism

A character. The name of the species the micrroarrays are measuring (e.g. 'homo_sapiens' or 'mus_musculus') given in lowercase and words separated by underscore.

arraytype

A character. Holds the platform name of the microarrays used in the analysis.

maxtargets

A numeric. The maximum number of allowed targets (e.g. genes or transcripts) one probe can have a match against. If to set it to 1 it means that the probe can match only one gene. If the analysis is set to 'transcript' the program still calculates the number of matches on genes. Hence a probe matching two transcripts on the same gene would be included but a probe matching two transcripts on different genes would not be included. The value needs to be a positive integer or 0.

maxprobes

A character. Sets the number of unique probes a target is allowed to have a match against. All the targets that yield more alignments to different probes then set by maxprobes will be scaled down to the number defined by the maxprobes parameter. It can be either a positive integer or set as 'median' or 'max' - 'median' meaning the median number of probes matching to all targets and 'max' meaning the maximum number of probes matching to a target.

pmsize

A numeric. The minimum number of consecutive nucleotides that need to match perfectly against the target sequence. It can be either 23, 24 or 25. This means that alignments with smaller perfect match size will not be included in the experiment.

sectionsize

A numeric. This is only used if the analysis parameter is set to 'genome'. It defines the length of the genomic target region used in the 'genome' analysis.

norm.method

A function. Defines a function used to normalize the raw expression values. The function should take in raw expression matrix and return the normalized expression matrix where probe ID's are kept as rownames and column names are CEL file names.

filetag

A character. This is a custom string that can be used to identify the experiment. At the current development stage this parameter is used only when using the function demi, where the output files will contain the specified filetag.

annoTable

A data.frame. Holds the annotation information used in the experiment.

blatTable

A data.frame. Holds the alignment information of probes and their corresponding targets.

cytoband

A data.frame. Only used in the 'genome' analysis. Holds the karyotype information for every chromosome of the species specified by the organism parameter.

pathway

A data.frame. Only used in the 'gene' and 'transcript' analysis. Holds the genes for every gene ontology category.

exprsdata

A DEMICel object. Holds the raw and normalized expression matrices in a DEMICel object.

results

A list. Can be used to store all the results as DEMIDiff objects done on the same DEMIExperiment object.

Author(s)

Sten Ilmjarv

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