Description Usage Arguments Details Value Author(s) References Examples
The algorithm first determines DCLs using a LFC model originally proposed for differential expression analysis, and then determines DCGs with their surrounding links enriched for DCLs.
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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. |
link.method |
a character string indicating link filtration method, default is 'qth'. |
cutoff |
cutoff used for link filtration, can be rth, qth, or percent depending on link.method. must be within [0,1]. |
r.method |
a character string indicating which correlation coefficient (or covariance) is to be computed. One of "pearson" (default) or "spearman", can be abbreviated. |
q.method |
a character string indicating which correction method to be utilized. the default is 'BH'. |
nbins |
number of x bins for fitting y=a+(b/x). |
p |
the cutoff of q-value; must be within [0,1]. |
figname |
names of figures of the LFC fitting results. |
DCe is based on the 'Limit Fold Change' or 'LFC' model, a robust statistical method originally proposed for selecting DEGs from microarray data (Mutch et al. 2002). With the analysis units changed from expression values to coexpression values, the LFC method with moderate adaption can be applied to screen for putative DCLs. DCGs with their surrounding links enriched for DCLs are determined through a binomial probability model.
A list with two components:
DCGs |
Differential Coexpression Genes |
DCLs |
Differential Coexpression Links |
Bao-Hong Liu, Hui Yu, Jing Yang
Mutch, D.M., Berger, A., Mansourian, R., Rytz, A. and Roberts, M.A. (2002) The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data, BMC Bioinformatics, 3, 17.
Yu H., Liu B-H., et al., Link-specific Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. Submitted. 2010
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All.links DC.links DCL_same DCL_diff DCL_switch p
CXCL13 47 23 10 11 2 2.239348e-11
MAP3K3 51 14 9 4 1 4.446182e-04
AGPAT1 35 10 7 2 1 2.047561e-03
q
CXCL13 2.239348e-09
MAP3K3 2.223091e-02
AGPAT1 6.825202e-02
Gene.1 Gene.2 cor.1 cor.2 type cor.diff
STK16,AACS STK16 AACS 0.534460299 0.01532619 same signed 0.5191341
BBOX1,FSTL1 BBOX1 FSTL1 -0.053121941 -0.38980386 same signed 0.3366819
DMC1,FSTL1 DMC1 FSTL1 -0.009651121 -0.25114129 same signed 0.2414902
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