Description Usage Arguments Details Value Author(s) Examples
A algorithm to select synthetical DCGs and DCLs from the results of DCp and DCe.
1 | DCsum(DCp.res, DCe.res, DCpcutoff = 0.25, DCecutoff = 0.25)
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DCp.res |
a data frame generated by DCp, with rows as genes and columns as 'dC' score, 'links', 'p.value' and 'q.value' value. |
DCe.res |
a list generated by DCe, with two components which are DCGs and DCLs. |
DCpcutoff |
the cutoff of 'q.vaule' in DCp results; must be within [0,1]; If there is no 'q.value' value (when N=0), 'dC' will be sorted in decreasing order and retained the highest by 'DCpcutoff' percent. |
DCecutoff |
the cutoff of 'q' in DCGs components of DCe results; must be within [0,1]. |
DCsum, short for Differentially Coexpression Summarization, summarizes 1) a set of DCGs, which is an intersection of DCp and DCe results; and 2) a set of DCLs which by definition must be connected with the DCGs. As a result, DCsum combines results from different coexpression analysis methods.
A list with two components:
DCGs |
Differentially Coexpressed Genes, combined two differential coexpression analysis |
DCLs |
Differentially Coexpressed Links, combined two differential coexpression analysis |
Jing Yang, Hui Yu
1 2 3 4 5 6 7 8 9 10 11 12 | data(exprs)
DCp.res<-DCp(exprs[1:100,1:16],exprs[1:100,17:63],
link.method = 'qth',cutoff=0.25)
DCe.res<-DCe(exprs[1:100,1:16],exprs[1:100,17:63],
link.method = 'qth',cutoff=0.25,nbins=20,p=0.1)
DCsum.res<-DCsum(DCp.res,DCe.res,DCpcutoff=0.25,DCecutoff=0.25)
## Differentially Coexpressed Genes after combination
DCsum.res$DCGs[1:3,]
## Differentially Coexpressed Links after combination
DCsum.res$DCLs[1:3,]
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