combineCOCOoutput {COCONUT} | R Documentation |
Combine COCONUT output from multiple objects into a single object. Makes pooled analysis of COCONUT-co-normalized data easier.
combineCOCOoutput(COCONUT.out)
COCONUT.out |
Output from a call to COCONUT(). |
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.
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. |
Timothy E Sweeney, MD, PhD (tes17 [at] stanford [dot] edu)
Sweeney TE et al., "Robust classification of bacterial and viral infections via integrated host gene expression diagnostics", 2016
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)