Description Usage Arguments Value Examples
This function identifies gene pairs coexpressed in at least one of two conditions.
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exprs.1 
a SummarizedExperiment, data frame or matrix for condition 1, with gene IDs as rownames and sample IDs as column names. 
exprs.2 
a SummarizedExperiment, data frame or matrix for condition 2, with gene IDs as rownames and sample IDs as column names. 
r.method 
a character string specifying the method to be used to calculate correlation coefficients. It is passed to the cor function of the WGCNA package. 
q.method 
a character string specifying the method for adjusting p values. It is passed to the p.adjust function of the stats package. 
rth 
the cutoff of absolute value of correlation coefficients; must be within [0,1]. 
qth 
the cutoff of qvalue (adjusted p value); must be within [0,1]. 
a data frame containing gene pairs that are coexpressed in at least one of the conditions with the criteria that absolute value of correlation coefficient is greater than rth and q value less than qth. It has the following columns:

Gene ID 

Gene ID 

correlation coefficients under condition 1 

correlation coefficients under condition 2 

difference between correlation coefficients under condition 2 and condition 1 

p value under null hypothesis that correlation coefficient under condition 1 equals to zero 

p value under null hypothesis that correlation coefficient under condition 2 equals to zero 

p value under null hypothesis that difference between two correlation coefficients under two conditions equals to zero using Fisher's rtoZ transformation 

adjusted p value under null hypothesis that correlation coefficient under condition 1 equals to zero 

adjusted p value under null hypothesis that correlation coefficient under condition 2 equals to zero 

adjusted p value under null hypothesis that the difference between two correlation coefficients under two conditions equals to zero using Fisher's rtoZ transformation 
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