SAGx (version 1.46.0)

clin2mim: Output a script file to WinMIM, linking clinical data and gene expression

Description

Given a clinical variable, it produces a script file for WinMIM by calculating means and covariances and for the N most highly correlated probes (in absolute value). Here N is an input parameter, but a recommended value 10. WinMIM can find a relevant graphical model for the dependencies between the probes and the clinical variable.

Usage

clin2mim(variable="FEV1.ACTUAL",data=dbs,clindat=clinical,probes=probes,N=10,out="mimscr.txt")

Arguments

variable

Clinical variable to be examined

data

The input data set, with subject id in first column.

clindat

The input clinical data, with subject id in first column

probes

The name of the probes in the order of data

N

The number of highly correlated probes to be studied

out

The MIM script file

Value

• The correlation matrix

References

Edwards, David (1995) Introduction to Graphical Modelling. Springer-Verlag Lautitzen, Steffen (1996) Graphical Models. Oxford University Press Whittaker, Joe (1990) Graphical Models in Multivariate Analysis. Wiley