runMFA: Function to perform a Multiple Factor Analysis.
In EMA: Easy Microarray Data Analysis

Description Usage Arguments Details Author(s) See Also Examples

This function allows to perform a Multiple Factor Analysis and to build a report with the main statistics and the main graphics.

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runMFA(Data, group = NULL, ncp = 5, name.group = NULL, type = NULL,
ind.sup = NULL, num.group.sup = NULL, graph = TRUE,
report.file = NULL, report.pdf = NULL)

`Data`	A data.frame or a list, see details
`group`	A vector indicating the number of variables in each group
`ncp`	Number of components to keep
`name.group`	Names of the groups of variables, default is NULL
`type`	the type of variables in each group; three possibilities: "c" or "s" for quantitative variables (the difference is that for "s" variables are scaled to unit variance), "n" for qualitative variables; by default, all variables are quantitative and scaled to unit variance
`ind.sup`	A vector indicating the indexes of the supplementary individuals
`num.group.sup`	The indexes of the illustrative groups (by default, NULL and no group are illustrative)
`graph`	boolean, if TRUE a graph is displayed
`report.file`	Name of the txt file for the text report
`report.pdf`	Name of the pdf file for the graphical report

Data can either be a data.frame with all the groups binded or a list containing all the groups such list(group1=group1, group2=group2, ...). In the case of a data.frame, group must be indicated.

The analysis report can also be build later by using functun MFAreport.

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe

MFA, plot.MFA, MFAreport

data(marty)
## Perform a MFA on splitted data
resMFA <- runMFA(Data=list(group1=t(marty[1:100,]),
group2=t(marty[101:200,])), type=c("c", "c"), graph=FALSE)
## Not run: 
## plot global analysis with partial individuals
plot(resMFA, choix="ind", partial="all")

## plot groups link
plot(resMFA, choix="group")

## End(Not run)