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README file for R package supporting the paper "Differential network analysis by simultaneously considering changes in gene interactions and gene expression". Contents of this archive ------------------------ This archive contains (1) pkg: subdirectory that contains the R package. (2) chNet-manual.pdf: reference manual. The chNet package has the following R-package dependencies: MASS, Matrix, igraph, mvtnorm, glmnet. The dependents are automatically installed along with chNet. You can use the following commands to install chNet from GitHub. # Step 1. Install the devtools package. Invoke R and then type install.packages("devtools") # Step 2. Load the devtools package. library("devtools") # Step 3. Install the chNet package from GitHub. install_github("TJJjiajuan/chNet", subdir="pkg") Useage Load the library chNet in R console, by running library(chNet) Taking the TCGA breast cancer datasets as an example, run the following code: data("TCGA.BRCA") result = chNet(TCGA.BRCA$X,TCGA.BRCA$group, lambar = 2.85, parallel = FALSE, nCpus = 4) Please do not hesitate to contact Dr. Xiao-Fei Zhang (zhangxf@mail.ccnu.edu.cn) or Miss Jia-Juan Tu (adaline_juan@mails.ccnu.edu.cn) to seek any clarifications regarding any contents or operation of the archive.
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