mixedModelDE: Run a mixed model on GeoMxSet

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Run a mixed model on GeoMxSet

Description

Run a mixed model on GeoMxSet

Usage

mixedModelDE(
  object,
  elt = "exprs",
  modelFormula = NULL,
  groupVar = "group",
  nCores = 1,
  multiCore = TRUE,
  pAdjust = "BY",
  pairwise = TRUE
)

Arguments

object	name of the object class to perform QC on NanoStringGeoMxSet, use the NanoStringGeoMxSet class
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

Value

mixed model output list

Examples

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
)

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.