iDINGO (version 1.0.4)

idingo: Fit iDINGO model

Description

This function fits the iDINGO model and calculates edge-wise differential scores for all pairwise edges among p variables between multiple platforms.

Usage

idingo(dat,dat2=NULL,dat3=NULL,x,plats=NULL,rhoarray=NULL,
        diff.score=T,B=100,verbose=T,cores=1)

Arguments

dat

nxp dataframe/matrix with colnames as genename

dat2

Second nxp dataframe/matrix with colnames as genename (optional)

dat3

Third nxp dataframe/matrix with colnames as genename (optional)

x

a length n vector representing a binary covariate

plats

a length 1-3 vector (corresponding to the number of data sets submitted, with names for the platforms/levels of the data, such as "microRNA" or "RNAseq". This is optional, and default names "platN" will be used if names are not provided.

rhoarray

a vector representing candidate tuning parameters of glasso for fitting global network model. If it is one value, then we use the value as the tuning parameter. It is set by NULL as default and we select 100 candidate values.

diff.score

a logical value. If TRUE, edge-wise differential scores are calculated from bootstrap standard error. Otherwise, we fit Steps 1 and 2 of DINGO model to get group specific GGMs (partial correlations)

B

the number of bootstrap samples to calculate differential scores.

verbose

if TRUE, lists the procedure

cores

the number of cores to run in parallel for bootstrapping, set to 1 as a default. If more cores are specified than the recommended maximum (the number of cores detected minus 1), this value will be replaced by the recommended value.

Value

genepair

a p(p-1)/2 x 2 matrix indicating all pairs of genes

levels.x

a length 2 vector indicating levels of the binary covariate x, the first element is for group 1 and the second element is for group 2

R1

a length p(p-1)/2 vector indicating partial correlations for group 1 and the order is corresponding to the order of genepair

R2

a length p(p-1)/2 vector indicating partial correlations for group 2 and the order is corresponding to the order of genepair

diff.score

a p(p-1)/2 vector of differential score corresponding to genepair

p.val

a p(p-1)/2 vector of corrected p-values corresponding to genepair

Examples

# NOT RUN {
data(brca)

# Run iDINGO with microRNA, RNA, and protein data.
# Generally, we recommend a minimum of 100 bootstraps.
# }
# NOT RUN {
fit <- idingo(brca$mirna, dat2 = brca$rna, dat3 = brca$prot,
    x = brca$class, plats = c("microRNA", "RNA", "Protein"),
    diff.score = TRUE, B = 20, cores = 2)
# }