Similarity Identification in Gene Expression

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Documentation for package ‘SIGN’ version 0.1.0

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BubbleSort BubbleSort is a function for calculating bubble sort correlation between two vectors
EventRenaming EventRenaming is a function for changing annotation of censored samples to 0 and dead samples to 1 for survival analysis
ExpPheno_Categorize ExpPheno_Categorize is a function for grouping samples based on their survival to 3 groups of poor, good, and intermediate
ExpPhen_Matching ExpPhen_Matching is a function for matching samples between expression matrices and metadata matrix (clinical feature matrix)
ExpPhen_Subdividing ExpPhen_Subdividing is a function for grouping samples based on a clinical feature available in metadata matrix (clinical feature matrix)
GeneMatching GeneMatching is a function to remove uncommon genes between a list of expression matrices
Genes_SimCal Genes_SimCal is a function to calculate similarity between a set of samples and 2 reference groups of samples
GSVA_Calculation GSVA_Calculation is a function for Calculating correlation between expression level of pathways between 2 groups using GSVA
Pathway_Grouping Pathway_Grouping is a function to make a pathway list from files containing genes within each pathway
Pathway_similarity Pathway_similarity is a function for calculating correlation between expression level of pathways between 2 groups using all the available approaches in SIGN
SIGN_Aggregate SIGN_Aggregate is a function to reshape the list of pathway scoring, time to death, and event and return a summary list
SIGN_Ensemble_SimCal SIGN_Ensemble_SimCal is a function for Generating list fo similarities based on different pathway quantification methods and similarity measures
Similarities_Wrapper Similarities_Wrapper is wrapper to identify similarities between the expression of genes in target sample and the reference expression matrix
SimSummary_2Class SimSummary_2Class is a function to calculating similarity between two set of samples
SurvivalStat_PostProcess SurvivalStat_PostProcess is a function to Extract summary statistics of the built cox model
Survival_Stats Survival_Stats is a function for building cox model using all the features and each feature as a separate model
TSC TSC is a function to calculate transcriprtional similarity coefficient between two biological pathways