Function reference • BioCor

General introduction

BioCor BioCor-package: BioCor: A package to calculate functional similarities

Similarity of pathways

Compare pairs of pathways, just one (pathSim) or as many as you want (mpathSim)

pathSim(): Calculates the Dice similarity between pathways

mpathSim(): Calculates the Dice similarity between pathways

Similarity of genes

Compare pairs of genes, just one (geneSim) or as many as you want (mgeneSim)

geneSim(): Similarity score genes based on pathways similarity

mgeneSim(): Similarity score genes based on pathways similarity

Pooling similarity of groups of genes

Compare groups of genes by pooling all the pathways they are in

clusterSim(): Similarity score between clusters of genes based on pathways similarity

mclusterSim(): Similarity score between clusters of genes based on pathways similarity

Similarity of groups of genes

Compare groups of genes by comparing the similarity of the genes in each group

clusterGeneSim(): Similarity score between clusters of genes based on genes similarity

mclusterGeneSim(): Similarity score between clusters of genes based on genes similarity

Convert between similarities

Convert from Jaccard to Dice or vice versa

D2J() J2D(): Convert the similarities formats

Combine similarities

combineScores() combineScoresPar(): Combining values

Helper functions

plot_data() plot_similarity(): The position of the nodes is based on the similarity between them.

combineSources(): Combine different sources of pathways

AintoB(): Insert a matrix into another

seq2mat(): Transforms a vector to a symmetric matrix

combinadic(): i-th combination of n elements taken from r

diceSim(): Compare pathways

duplicateIndices(): Finds the indices of the duplicated events of a vector

removeDup(): Remove duplicated rows and columns

inverseList(): Invert a list

similarities(): Apply a function to a list of similarities

addSimilarities(): Additive integration of similarities

weighted.sum() weighted.prod(): Weighted operations