Transcriptional analysis based on transcriptograms


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Documentation for package ‘transcriptogramer’ version 1.18.0

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transcriptogramer-package Transcriptional analysis based on transcriptograms
association Association
clusterEnrichment Term enrichment
clusterEnrichment-method Term enrichment
clusterVisualization Displays graphs of the differentially expressed clusters
clusterVisualization-method Displays graphs of the differentially expressed clusters
connectivityProperties Calculates average graph properties as function of node connectivity
connectivityProperties-method Calculates average graph properties as function of node connectivity
DE Get DE
DE-method Get DE
DEsymbols Dictionary Protein2Symbol
differentiallyExpressed Identify which genes are differentially expressed
differentiallyExpressed-method Identify which genes are differentially expressed
enrichmentPlot Projects Gene Ontology terms on the ordering
enrichmentPlot-method Projects Gene Ontology terms on the ordering
GPL570 Dictionary Protein2Probe
GSE9988 Dataset containing expression values
Hs700 Ordered Homo sapiens proteins of combined score greater than or equal to 700
Hs800 Ordered Homo sapiens proteins of combined score greater than or equal to 800
Hs900 Ordered Homo sapiens proteins of combined score greater than or equal to 900
HsBPTerms Dictionary Protein2GO
Mm700 Ordered Mus musculus proteins of combined score greater than or equal to 700
Mm800 Ordered Mus musculus proteins of combined score greater than or equal to 800
Mm900 Ordered Mus musculus proteins of combined score greater than or equal to 900
orderingProperties Calculates graph properties projected on the ordered proteins
orderingProperties-method Calculates graph properties projected on the ordered proteins
radius Radius
radius-method Radius
radius<- Radius
radius<--method Radius
Rn700 Ordered Rattus norvegicus proteins of combined score greater than or equal to 700
Rn800 Ordered Rattus norvegicus proteins of combined score greater than or equal to 800
Rn900 Ordered Rattus norvegicus proteins of combined score greater than or equal to 900
Sc700 Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700
Sc800 Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800
Sc900 Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900
Terms Get terms
Terms-method Get terms
Transcriptogram-class Class Transcriptogram
transcriptogramer Transcriptional analysis based on transcriptograms
transcriptogramPreprocess Creates an object of class Transcriptogram
transcriptogramStep1 Calculates the average of the expression values related to the same protein
transcriptogramStep1-method Calculates the average of the expression values related to the same protein
transcriptogramStep2 Calculates the average of the expression values using a sliding window
transcriptogramStep2-method Calculates the average of the expression values using a sliding window