gene.trait.similarity: Calculate similarity for gene-trait interaction

In BUS: Gene network reconstruction

Description

To calculate similarity for gene-trait interaction (using correlation/mutual information metric).

Usage

gene.trait.similarity(EXP, trait, measure, na.replica = 50)

Arguments

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.

Value

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.

Author(s)

Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini

Examples

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")

Example output

Loading required package: minet
                            hsa-let-7b hsa-let-7c hsa-let-7e hsa-let-7i
AFFX-HUMISGF3A/M97935_MB_at 0.03164175  0.0000000  0.5344331  0.1247663
AFFX-HUMISGF3A/M97935_3_at  0.03164175  0.0000000  0.0000000  0.1247663
AFFX-HSAC07/X00351_5_at     0.03164175  0.0000000  0.0000000  0.1247663
200001_at                   0.03164175  0.0000000  0.0000000  0.0000000
200003_s_at                 0.03164175  0.1247663  0.1247663  0.0000000
200006_at                   0.03164175  0.1247663  0.0000000  0.0000000
200008_s_at                 0.29885832  0.1247663  0.0000000  0.1247663
200009_at                   1.00000000  0.1247663  0.1247663  0.1247663
200013_at                   0.03164175  0.1247663  0.5344331  0.1247663
200014_s_at                 0.03164175  0.1247663  0.1247663  0.0000000
                            hsa-mir-100
AFFX-HUMISGF3A/M97935_MB_at  0.03164175
AFFX-HUMISGF3A/M97935_3_at   0.03164175
AFFX-HSAC07/X00351_5_at      0.03164175
200001_at                    0.29885832
200003_s_at                  0.03164175
200006_at                    0.03164175
200008_s_at                  0.03164175
200009_at                    0.03164175
200013_at                    0.29885832
200014_s_at                  0.03164175

BUS documentation built on Nov. 8, 2020, 6:55 p.m.