View source: R/NanoStringGeoMxSet-de.R
mixedModelDE | 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")
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 = 2,
multiCore = TRUE,
pAdjust = NULL
)
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