ConditionSpecificGenes: Condition specifically expressed genes

In mlDNA: Machine Learning-based Differential Network Analysis of Transcriptome Data

Description

This function detects condition specifcally expressed genes which are highly expressed in only one condition (e.g., stress), but are not or lowly expressed in the other conditions.

Usage

ConditionSpecificGenes( expmat, logtransformed = TRUE, base = 2, threshold = 0.75 ) 

Arguments

expmat	a numeric matrix recording the expression level of genes at different conditions. The column labels are samples names. For two samples from the same condition C, their names should be assigned as C.1 and C.2, respectively.
logtransformed	logical indicating whether the gene expression values in expmat have been log-transformed.
base	a numeric value indicating the base of logarithm.
threshold	a numeric value giving the threshold of condition specificity score. The condition specificity score is 1, if the gene is only expressed at one condition. Otherwise, the condition specificity socre will be smaller than 1.

Value

A list with following components:

CSGenes	a character vector containing the condition specially expressed genes.
CSScoreMat	a data matrix recording the condition-specificity scores for all condtions, the maximal condition-specificity score and its corresponding condition"
uniqueCS	a data matrix containing the condition informaiton obtained from the colnames(expmat).

Author(s)

Chuang Ma, Xiangfeng Wang

References

[1] Chuang Ma, Xiangfeng Wang. Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis thaliana. 2013(Submitted).

Examples

## Not run: 
  
   ##show colnames of SaltExpMat
   colnames(SaltExpMat)

   ##as the dot is used to indicate the replications in one condition, we 
   ##have to change the colname of genes at the 0.5 time point.
   colnames(SaltExpMat)[1] <- "Salt_0_5h"

   ##get condition specifically expressed genes
   res <- ConditionSpecificGenes( expmat = SaltExpMat, logtransformed = TRUE, 
                                  base = 2, threshold = 0.75 ) 

   ##number of condition specifically expressed genes
   length(res$CSGenes)
 
## End(Not run)  

mlDNA documentation built on May 2, 2019, 2:15 p.m.