Description Usage Arguments Details Value Author(s) References Examples
The algorithm to rank candidate regulators
1 2 3 4 | RIF(exprs, exprs.1, exprs.2,
tf2target,
exprs_design,
p.value)
|
exprs |
a data frame or matrix for expression dataset, with rows as variables (genes) and columns as samples. |
exprs.1 |
a data frame or matrix for condition A, with rows as variables (genes) and columns as samples. |
exprs.2 |
a data frame or matrix for condition B, with rows as variables (genes) and columns as samples. |
tf2target |
a data frame or matrix for regulator-to-target interaction pairs. |
exprs_design |
a data frame or matrix for displaying microarray experiment design. |
p.value |
a p value threshold to determine differential expression genes (DEGs). |
RIF method, short for 'Regulator Impact Factor' (Reverter etal. 2010), assesses the change of regulation-accountable expression value of Differentially Expressed Genes (DEGs) and correlation coefficient between DEGs and TFs to rank TFs.
A matrix to display RIF scores and ranks.
Jing Yang, Hui Yu
Reverter, A., Hudson, N. J., Nagaraj, S. H., Perez-Enciso, M., Dalrymple, B. P. (2010) Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data, 26, 896-904.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | data(exprs)
## divide exprs into two parts corresponding to condition 1
## (exprs.1) and condition 2 (exprs.2) respectively
exprs<-exprs[1:100,]
exprs.1<-exprs[1:100,1:16]
exprs.2<-exprs[1:100,17:63]
DCp.res<-DCp(exprs.1,exprs.2,
link.method = 'qth',cutoff=0.25)
DCe.res<-DCe(exprs.1,exprs.2,
link.method = 'qth',cutoff=0.25,nbins=10,p=0.1)
DCsum.res<-DCsum(DCp.res,DCe.res,DCpcutoff=0.25,DCecutoff=0.4)
## rank all the potential TFs
data(tf2target)
data(exprs_design)
RIF.res<-RIF(exprs,exprs.1,exprs.2,
tf2target,
exprs_design,
p.value=0.05)
RIF.res[1:3,]
|
TF RIF_score RIF_rank
1 ZEB1 3.96066292 1
2 EP300 3.33968659 2
3 MAX -0.07059944 3
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