Description Usage Arguments Value
Compute the Connectivity Scores by Zhang and Gant (2008). One or multiple query compounds are possible in this analysis. In the case of multiple query compounds, the average of each pairwise score is taken.
1 2 3 4 5 6 7 | ## S4 method for signature 'matrix,matrix,CSzhang'
CSanalysis(querMat, refMat,
type = "CSzhang", nquery = NULL, nref = NULL, ntop.scores = 20,
which = c(1), color.ref = NULL, legend.names = NULL,
legend.cols = NULL, legend.pos = "topright", labels = TRUE,
result.available = NULL, result.available.update = FALSE,
plot.type = "device", basefilename = NULL)
|
querMat |
Query matrix (Rows = genes and columns = compounds) |
refMat |
Reference matrix |
type |
|
nquery |
Zhang Parameter: Number of top up- and downregulated genes in query signature. If |
nref |
Zhang Parameter: Number of top up- and downregulated genes in reference signature. If |
ntop.scores |
Zhang Parameter: Number of top positive and negative CS to be reported first. |
which |
Choose plot to draw.
|
color.ref |
Vector of colors for the reference columns. You can use this option to highlight columns(compounds) of interest in the CS plot. (This does not include the query columns since they are not included in the CS plot.) |
legend.names |
Option to draw a legend (about the highlights in |
legend.cols |
Colors to be used for the |
legend.pos |
Position of the legend in all requested plots, can be |
labels |
Boolean value (default=TRUE) to use column labels inside the ZG plot. |
result.available |
You can a previously returned object by |
result.available.update |
Logical value. If |
plot.type |
How should the plots be outputted? |
basefilename |
Directory including filename of the graphs if saved in pdf files |
An object of the S4 Class CSresult-class
. The CS slot will also contain the top positive and negative scores as well as the top p-values. The GS slot will be empty for Zhang and Gant.
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