pathdiagram: Path Diagram

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Create a directed acyclic diagram to represent causal effects of risk factors on the disease of study.

Usage

1
pathdiagram(pathdata, disease, R2, range)

Arguments

pathdata

R object that is dataset consisting of correlation matrix of risk factors and a numeric vector of direct path coefficients.

disease

a string that specifies outcome name or disease name. If disease name is long or has multiple words, then we suggest an abbreviated name, for example, coronary artery disease may be shortened as CAD.

R2

a numeric parameter, is R-square obtained from path analysis.

range

range of specified columns for correlation matrix. For example, range = c(2:4) means the correlation coefficient begins with column 2 and end at column 4.

Details

The pathdata contains correlation matrix of risk factors and a numeric vector of direct path coefficients obtained from path analysis of beta data of SNPs on risk factors and disease. Columns must have risk factor names and path.

Value

NULL. pathdiagram will create one-level path diagram labeled with colors.

Author(s)

Yuan-De Tan tanyuande@gmail.com

\Dajiang Liu

See Also

pathdiagram2, plotmat, plotweb

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
mypath<-matrix(NA,3,4)
mypath[1,]<-c(1.000000,-0.066678, 0.420036,0.764638)
mypath[2,]<-c(-0.066678,1.000000,-0.559718,0.496831)
mypath[3,]<-c(0.420036,-0.559718,1.000000,0.414346)
colnames(mypath)<-c("ldl","hdl","tg","path")

#mypath
#        ldl       hdl        tg      path
#1  1.000000 -0.066678  0.420036  0.764638
#2 -0.066678  1.000000 -0.559718  0.496831
#3  0.420036 -0.559718  1.000000  0.414346

mypath<-as.data.frame(mypath)
pathdiagram(pathdata=mypath,disease="cad",R2=0.988243,range=c(1:3))


Search within the GMRP package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.