Description Usage Arguments Value
Compute the Connectivity Scores by Zhang and Gant (2008). One or multiple reference compounds are possible in this analysis.
1 2 3 4 5 6 7 | ## S4 method for signature 'matrix,matrix,CSzhang'
CSanalysis(refMat, querMat,
type = "CSzhang", nref = NULL, nquery = NULL, ord.query = TRUE,
ntop.scores = 20, which = c(1), color.query = NULL,
legend.names = NULL, legend.cols = NULL, legend.pos = "topright",
result.available = NULL, result.available.update = FALSE,
plot.type = "device", basefilename = "analyseZhang")
|
refMat |
Reference matrix (Rows = genes and columns = compounds) |
querMat |
Query matrix |
type |
|
nref |
Zhang Parameter: Number of top up- and downregulated genes in reference signature. If |
nquery |
Zhang Parameter: Number of top up- and downregulated genes in query signature. If |
ord.query |
Zhang Parameter: Logical value. Should the query signature be treated as ordered? |
ntop.scores |
Zhang Parameter: Number of top positive and negative CS to be reported first. |
which |
Choose plot to draw.
|
color.query |
Vector of colors for the query columns. You can use this option to highlight columns(compounds) of interest in the CS plot. (This does not include the reference 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 |
result.available |
You can a previously returned object by |
result.available.update |
Logical value. If |
plot.type |
How should the plots be outputted? |
basefilename |
Basename of the graphs if saved in pdf files |
An object of the S4 Class CSresult
. 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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