Description Usage Arguments Value Examples
This function calculates correlation coefficients of all gene pairs under two conditions and compare them using Fisher's Ztransformation.
1 2 3  comparecor(exprs.1, exprs.2, r.method = c("pearson", "spearman")[1],
q.method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr",
"none")[1])

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. 
a data frame containing the differences between the correlation coefficients under two consitions and their p values. 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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