defacto | R Documentation |
This function helps the user to describe and interpret the factors using some available external information on either genes or arrays. Diagnostic plots are provided.
defacto(model, plot = TRUE, axes = c(1, 2), select.covar = NULL, select.annot = NULL, lim.b = 0.01, lab = TRUE, cex = 1)
model |
'FAMTmodel' object |
plot |
Boolean (TRUE by default). If TRUE, diagnostic plots are provided (unless the 'FAMTmodel' has less than one factor). |
axes |
Vector of length 2, specifying the factors to plot. |
select.covar |
Selection of external covariates. If NULL (default value), the function takes all covariates except the array identifiers and those used in the model. |
select.annot |
Selection of external annotations. If NULL (default value), the function takes all the available factors in 'annotations'. |
lim.b |
Proportion of variables with the highest loadings for each factor to appear on plots or in tables (0.01 by default). |
lab |
Boolean. If TRUE (default value), array names are labeled on the figure |
cex |
A numerical value giving the amount by which plotting text and symbol should be enlarged relative to the default (1 is the default value) |
loadings |
highest loadings (B matrix) for each factor. The proportion of loading is determined by "lim.b" |
covariates |
Matrix of p-values for the tests of linear relationships between scores on each factor (rows) and external covariates (columns). |
annotations |
Matrix of p-values for the tests of linear relationships between loadings of each factor (rows) and external annotations (columns). |
David Causeur, Maela Kloareg
as.FAMTdata
, modelFAMT
## FAMT data data(expression) data(covariates) data(annotations) # Create the 'FAMTdata' ############################################ chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2) # 'FAMTdata' summary ## Not run: summaryFAMT(chicken) # FAMT complete multiple testing procedure ############################################ model = modelFAMT(chicken,x=c(3,6),test=6,nbf=3) # summary on the 'FAMT model' ## Not run: summaryFAMT(model) # Factors description ############################################ chicken.defacto = defacto(model,axes=1:2,select.covar=4:5,select.annot=3:6, cex=0.6)
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