Description Usage Arguments Value
Doing interactive CS analysis with sMFA (Sparse Multiple Factor Analysis). Should use multiple queries for this analysis.
Either spca
or arrayspc
is used.
1 2 3 4 5 6 7 8 9 10 11 12 | ## S4 method for signature 'matrix,matrix,CSsmfa'
CSanalysis(querMat, refMat, type = "Csmfa",
K = 15, para, lambda = 1e-06, sparse.dim = 2, sparse = "penalty",
max.iter = 200, eps.conv = 0.001, which = c(2, 3, 4, 5),
component.plot = NULL, CSrank.queryplot = FALSE, column.interest = NULL,
row.interest = NULL, profile.type = "gene", color.columns = NULL,
gene.highlight = NULL, gene.thresP = 1, gene.thresN = -1,
thresP.col = "blue", thresN.col = "red", grouploadings.labels = NULL,
grouploadings.cutoff = 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 |
|
K |
sMFA Parameters: Number of components. |
para |
sMFA Parameters: A vector of length K. All elements should be positive. If |
lambda |
sMFA Parameters: Quadratic penalty parameter. Default value is 1e-6. If the target dimension of the sparsness is higher than the other dimension (p > n), it is advised to put |
sparse.dim |
sMFA Parameters: Which dimension should be sparse? 1: Rows, 2: Columns (default) (Note: For Connectivity Scores it is advised to apply sparsity on the compounds/columns) |
sparse |
sMFA Parameters ( |
max.iter |
sMFA Parameters: Maximum number of iterations. |
eps.conv |
sMFA Parameters: Convergence criterion. |
which |
Choose one or more plots to draw:
|
component.plot |
Which components (Factor/Bicluster) should be investigated? Can be a vector of multiple (e.g. |
CSrank.queryplot |
Logical value deciding if the CS Rank Scores ( |
column.interest |
Numeric vector of indices of reference columns which should be in the profiles plots ( |
row.interest |
Numeric vector of gene indices to be plotted in gene profiles plot ( |
profile.type |
Type of
|
color.columns |
Vector of colors for the query and reference columns (compounds). If |
gene.highlight |
Single numeric vector or list of maximum 5 numeric vectors. This highlights gene of interest in gene scores plot ( |
gene.thresP |
Threshold for genes with a high score ( |
gene.thresN |
Threshold for genes with a low score ( |
thresP.col |
Color of genes above |
thresN.col |
Color of genes below |
grouploadings.labels |
This parameter used for the Group Loadings Plots (
Plot Please note that even when |
grouploadings.cutoff |
Parameter used in plot |
legend.names |
Option to draw a legend of for example colored columns in Compound Loadings plot ( |
legend.cols |
Colors to be used in legends. If |
legend.pos |
Position of the legend in all requested plots, can be |
labels |
Boolean value (default=TRUE) to use row and/or column text labels in the score plots ( |
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
.
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