gene.trait.similarity {BUS} | R Documentation |
To calculate similarity for gene-trait interaction (using correlation/mutual information metric).
gene.trait.similarity(EXP, trait, measure, na.replica = 50)
EXP |
Gene expression data in form of a matrix. Row stands for genes and column for experiments. |
trait |
Trait data in form of matrix. Row stands for traits and column for experiments. |
measure |
Metric used to calculate similarity: "corr" for correlation, "MI" for mutual information. |
na.replica |
Times of replicates for filling NANs in impute method; default value is 50. The (smooth) bootstrapping approach is used to give an estimation to missing value in the data. |
A matrix, row stands for gene and column for trait. Element in row i and column j stands for the association between the gene i and trait j.
Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini
data(tumors.mRNA) data(tumors.miRNA) exp<-tumors.mRNA trait<-tumors.miRNA gene.trait.similarity(EXP= exp[1:10, ],trait= trait[1:5, ],measure="MI")