gene.trait.pvalue: Calculate p-value for gene-trait interaction
In BUS: Gene network reconstruction

Description Usage Arguments Details Value Author(s) See Also Examples

To calculate p-value for null hypothesis that there is no interaction between gene and trait. There are MxT interactions between M genes and T traits. Results are given with 3 possibilities 1 for single p-value, and 3 for different types of correction. p-values are calculated based on the adjacency matrix for gene-gene interaction computed by function gene.trait.similarity.

1	gene.trait.pvalue(EXP, trait, measure, method.permut = 2, n.replica = 400)

`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.
`method.permut`	A flag to indicate correction style when multiple hypotheses testing is considered. 1 for multiple traits correction, 2 for multiple genes and 3 for both genes and traits correction. The default value is 2.
`n.replica`	Number of permutations for the correction of multiple hypothesis testing; default value is 400.

According to a permutation method, we use the empirical distribution of some statistics to estimate the p-value. For single p-value the empirical distribution is a vector of P (number of random replicates for each test) test values. It is then possible to correct p-value in different ways: method.permut = 1, it is the empirical distribution of a vector with length of TxP, corrects for the multiple traits tested; method.permut = 2, it is the empirical distribution of a vector with length of MxP, corrects for the multiple genes tested; method.permut = 3, it is empirical distribution of a vector with length of MxTxP, corrects for the multiple traits and genes tested.

`single.perm.p.value`	A matrix of single p-values obtained with permutation method + beta distribution for extreme values (for MI) or obtained with the exact distribution computed directly by cor.test (for correlation)
`multi.perm.p.value`	A matrix of corrected p-values obtained with permutation method

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

gene.trait.similarity

data(tumors.mRNA)
data(tumors.miRNA)
exp<-tumors.mRNA
trait<-tumors.miRNA
gene.trait.pvalue(EXP=exp[1:10,],trait=trait[1:5,],measure="MI")

Loading required package: minet
$single.perm.p.value
                            hsa-let-7b hsa-let-7c hsa-let-7e hsa-let-7i
AFFX-HUMISGF3A/M97935_MB_at     0.7825     0.5975     0.0625     0.4825
AFFX-HUMISGF3A/M97935_3_at      0.7725     0.5875     0.5500     0.4700
AFFX-HSAC07/X00351_5_at         0.7775     0.6075     0.5825     0.4775
200001_at                       0.7650     0.5525     0.5400     0.5225
200003_s_at                     0.7625     0.4225     0.3850     0.5300
200006_at                       0.7500     0.3900     0.5775     0.5675
200008_s_at                     0.2050     0.3825     0.5800     0.4225
200009_at                       0.0000     0.4225     0.4925     0.4850
200013_at                       0.7550     0.4275     0.0725     0.4575
200014_s_at                     0.7475     0.4325     0.5000     0.5500
                            hsa-mir-100
AFFX-HUMISGF3A/M97935_MB_at      0.7700
AFFX-HUMISGF3A/M97935_3_at       0.7850
AFFX-HSAC07/X00351_5_at          0.7650
200001_at                        0.1500
200003_s_at                      0.7625
200006_at                        0.7575
200008_s_at                      0.7600
200009_at                        0.7700
200013_at                        0.1650
200014_s_at                      0.7550

$multi.perm.p.value
                            hsa-let-7b hsa-let-7c hsa-let-7e hsa-let-7i
AFFX-HUMISGF3A/M97935_MB_at    0.76725    0.57375    0.05825    0.46225
AFFX-HUMISGF3A/M97935_3_at     0.76725    0.57375    0.55525    0.46225
AFFX-HSAC07/X00351_5_at        0.76725    0.57375    0.55525    0.46225
200001_at                      0.76725    0.57375    0.55525    0.55675
200003_s_at                    0.76725    0.42275    0.41400    0.55675
200006_at                      0.76725    0.42275    0.55525    0.55675
200008_s_at                    0.18775    0.42275    0.55525    0.46225
200009_at                      0.00000    0.42275    0.46875    0.46225
200013_at                      0.76725    0.42275    0.05825    0.46225
200014_s_at                    0.76725    0.42275    0.46875    0.55675
                            hsa-mir-100
AFFX-HUMISGF3A/M97935_MB_at      0.7660
AFFX-HUMISGF3A/M97935_3_at       0.7660
AFFX-HSAC07/X00351_5_at          0.7660
200001_at                        0.1735
200003_s_at                      0.7660
200006_at                        0.7660
200008_s_at                      0.7660
200009_at                        0.7660
200013_at                        0.1735
200014_s_at                      0.7660