lincsTools: Run Shane's LINCS Tools on MetaIntegrator

In MetaIntegrator: Meta-Analysis of Gene Expression Data

Description

Run Shane's LINCS Tools on MetaIntegrator

Usage

lincsTools(metaObject, filterObject, report.out.folder,
  hit.number.hm = 10, hit.number.tbl = 10, resize = F,
  reportTitle = "lincsReport")

Arguments

metaObject	a Meta object which must have the $originalData populated
filterObject	a MetaFilter object containing the signature genes that will be used for calculating the score
report.out.folder	Directory where a report with all figures and tables will be generated.
hit.number.hm	How many hits to show in a heatmap (default:10)
hit.number.tbl	How many hits to show in a displayed table (default:10)
resize	Whether to resize tables in the way Purvesh prefers for figures (default: FALSE)
reportTitle	file prefix for report outputs (default: "lincsReport")

Value

LINCS report for the data

Examples

## Not run: 
####### DATA SETUP ##########
# Example won't work on tinyMetaObject because it requires real gene names
# Download the needed datasets for processing. 
sleData <- getGEOData(c("GSE11909","GSE50635", "GSE39088"))

#Label classes in the datasets
sleData$originalData$GSE50635 <- classFunction(sleData$originalData$GSE50635, 
  column = "subject type:ch1", diseaseTerms = c("Subject RBP +", "Subject RBP -"))
sleData$originalData$GSE11909_GPL96 <- classFunction(sleData$originalData$GSE11909_GPL96, 
   column = "Illness:ch1", diseaseTerms = c("SLE"))
sleData$originalData$GSE39088 <- classFunction(sleData$originalData$GSE39088, 
   column= "disease state:ch1", diseaseTerms=c("SLE"))
 #Remove the GPL97 platform that was downloaded
sleData$originalData$GSE11909_GPL97 <- NULL

#Run Meta-Analysis
sleMetaAnalysis <- runMetaAnalysis(sleData, runLeaveOneOutAnalysis = F, maxCores = 1)

#Filter genes
sleMetaAnalysis <- filterGenes(sleMetaAnalysis, isLeaveOneOut = F, 
   effectSizeThresh = 1, FDRThresh = 0.05)
####### END DATA SETUP ##########

# Run immunoStates
 lincsTools(influenzaMeta, influenzaMeta$filterResults$FDR0.05_es0_nStudies4_looaTRUE_hetero0)

## End(Not run)

MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.