coexpr: Identification of gene pairs coexpressed in at least one of...

In hidelab/diffcoexp: Differential Co-expression Analysis

Identification of gene pairs coexpressed in at least one of two conditions

Description

This function identifies gene pairs coexpressed in at least one of two conditions.

Usage

coexpr(exprs.1, exprs.2, r.method = c("pearson", "spearman")[1],
  q.method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr",
  "none")[1], rth = 0.5, qth = 0.1)

Arguments

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 q-value (adjusted p value); must be within [0,1].

Value

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.1	Gene ID
Gene.2	Gene ID
cor.1	correlation coefficients under condition 1
cor.2	correlation coefficients under condition 2
cor.diff	difference between correlation coefficients under condition 2 and condition 1
p.1	p value under null hypothesis that correlation coefficient under condition 1 equals to zero
p.2	p value under null hypothesis that correlation coefficient under condition 2 equals to zero
p.diffcor	p value under null hypothesis that difference between two correlation coefficients under two conditions equals to zero using Fisher's r-to-Z transformation
q.1	adjusted p value under null hypothesis that correlation coefficient under condition 1 equals to zero
q.2	adjusted p value under null hypothesis that correlation coefficient under condition 2 equals to zero
q.diffcor	adjusted p value under null hypothesis that the difference between two correlation coefficients under two conditions equals to zero using Fisher's r-to-Z transformation

Examples

data(gse4158part)
allowWGCNAThreads()
res=coexpr(exprs.1 = exprs.1, exprs.2 = exprs.2, r.method = "spearman")
#The result is a data frames.
str(res)

hidelab/diffcoexp documentation built on April 20, 2024, 4:30 p.m.