COCONUT (version 1.0.1)

combineCOCOoutput: Combine COCONUT output from multiple objects into a single object

Description

Combine COCONUT output from multiple objects into a single object. Makes pooled analysis of COCONUT-co-normalized data easier.

Usage

combineCOCOoutput(COCONUT.out)

Arguments

COCONUT.out

Output from a call to COCONUT().

Value

This function will knit all data together into a list with three parts:

gene

contains a single matrix with all COCONUT-conormalized data (both control and disease)

pheno

contains a single data.frame with all phenotype info from the input samples, but ONLY from those columns whose colnames are same across all cohorts

class.cntl0.dis1

a binary vector that contains control/disease assignment for all columns in $genes.

Details

The output from COCONUT() can be a bit daunting, and the separate dataobjects remain separated by input cohort, plus are separated into control and diseased components.

References

Sweeney TE et al., "Robust classification of bacterial and viral infections via integrated host gene expression diagnostics", 2016

Examples

data(GSEs.test)

## apply COCONUT to a very small test case
## (3 datasets with 10 patients and 2000 genes)
GSEs.COCONUT <- COCONUT(GSEs=GSEs.test,
                        control.0.col="Healthy0.Sepsis1",
                        byPlatform=FALSE)

## combine output
GSEs.COCO.combined <- combineCOCOoutput(GSEs.COCONUT)
str(GSEs.COCO.combined)