mixedModelDE {GeomxTools} | R Documentation |
Run a mixed model on GeoMxSet
mixedModelDE( object, elt = "exprs", modelFormula = NULL, groupVar = "group", nCores = 1, multiCore = TRUE, pAdjust = "BY", pairwise = TRUE )
object |
name of the object class to perform QC on
|
elt |
assayDataElement of the geoMxSet object to run the DE on |
modelFormula |
formula used in DE, if null, the design(object) is used |
groupVar |
= "group", sample annotation to group the data for comparing means |
nCores |
= 1, number of cores to use, set to 1 if running in serial mode |
multiCore |
= TRUE, set to TRUE to use multiCore, FALSE to run in cluster mode |
pAdjust |
= "BY" method for p-value adjustment |
pairwise |
boolean to calculate least-square means pairwise differences |
mixed model output list
datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools") demoData <- readRDS(file.path(datadir, "/demoData.rds")) target_demoData <- aggregateCounts(demoData) target_demoData <- normalize(target_demoData, norm_method="quant") target_demoData <- target_demoData[1:100, ] pData(target_demoData)[["slide"]] <- factor(pData(target_demoData)[["slide name"]]) protocolData(target_demoData)[["pool_rep"]] <- factor(protocolData(target_demoData)[["pool_rep"]]) mixedOutmc <- mixedModelDE(target_demoData, elt = "exprs_norm", modelFormula = ~ pool_rep + (1 | slide), groupVar = "pool_rep", nCores = 12, multiCore = TRUE, pAdjust = NULL )