StarBioTrek

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Documentation for package ‘StarBioTrek’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

StarBioTrek-package	Download data
average	For TCGA data get human pathway data and creates a matrix with the average of genes for each pathway.
circleplot	Preparation for circle plot
ConvertedIDgenes	Get interacting genes inside pathways.
dsscorecrtlk	For TCGA data get human pathway data and creates a measure of discriminating score among pathways
eucdistcrtlk	For TCGA data get human pathway data and creates a measure of cross-talk among pathways
GetData	Get general information inside pathways.
getNETdata	Get network data from GeneMania.
GetPathData	Get genes inside pathways.
GetPathNet	Get interacting genes inside pathways.
GE_matrix	Get human KEGG pathway data and a gene expression matrix in order to obtain a list with the gene expression for only pathways given in input .
GE_matrix_mean	Get human KEGG pathway data and a gene expression matrix in order to obtain a matrix with the mean gene expression for only pathways given in input .
GOChord	Displays the relationship between genes and terms.
IPPI	Multilayer analysis Cava et al. BMC Genomics 2017
listpathnet	Get human KEGG pathway data and the output of list_path_net define the common genes.
pathnet	Get human KEGG pathway data and creates a network data.
plotcrosstalk	Preparation for plotting cross-talk
SelectedSample	Select the class of TCGA data
select_class	Select the class of TCGA data
StarBioTrek	Download data
stdv	For TCGA data get human pathway data and creates a measure of standard deviations among pathways
svm_classification	SVM classification for each feature