pathwayRF(pathwayRF)R Documentation

Pathway analysis using Random Forests

Description

Pathway analysis using Random Forests classification and regression.

Usage

PathwayRF <- function(clsfile, gmtfile, gctfile, numoftree, range, categorical)

PathwayRFimp  <- function(clsfile, gmtfile, gctfile, numoftree, pathwaynum, categorical)

Arguments

clsfile a phenotype data file.
gmtfile a pathway/geneset file.
gctfile a gene expression data file.
numoftree number of trees used for each iteration of Random Forests run.
range enter the rows from your gmt file to perform RF pathway analysis.
categorical specify whether your input cls file is categorical phenotype or not.
pathwaynum the line number of the pathway in gmt

Author(s)

Herbert Pang <pathwayRF@gmail.com> and Hongyu Zhao <hongyu.zhao@yale.edu>

References

o
Pang H, Lin A, Holford M, Enerson BE, Lu B, Lawton MP, Floyd E, Zhao H. Pathway analysis using random forests classification and regression. Bioinformatics. 2006 Aug 15;22(16):2028-36.
http://people.duke.edu/~hp44/rf.htm

See Also

randomForest.

Examples

## load example data
cls_location <- url("http://people.duke.edu/~hp44/data/breast.cls")
gmt_location <- url("http://people.duke.edu/~hp44/data/breast.gmt")
gct_location <- url("http://people.duke.edu/~hp44/data/breast.gct")
## run Random Forests pathway analysis with 5000 trees
## using the canine data
## looking at pathway 1 to 10
PathwayRF(cls_location, gmt_location, gct_location, 5000, 1:10, TRUE)
## save your output in an object called myresults
myresults <- PathwayRF(cls_location, gmt_location, gct_location, 5000, 1:10, TRUE)
## calling myresults
myresults
[Package pathwayRF version 1.0 Index]