Nothing
## ----options, cache=FALSE, include=FALSE, results='hide', message=FALSE, warning=FALSE----
knitr::opts_chunk$set(fig.align="center",
cache=FALSE,
error=FALSE,
fig.width=6,fig.height=6,
autodep=TRUE,
out.width="600px",
out.height="600px",
message=FALSE,
warning=FALSE,
results="hide",
echo=TRUE,
eval=TRUE)
options(getClass.msg=FALSE)
## ----case-only-------------------------------------------------------------
library(ImpulseDE2)
lsSimulatedData <- simulateDataSetImpulseDE2(
vecTimePointsA = rep(seq(1,8),3),
vecTimePointsB = NULL,
vecBatchesA = NULL,
vecBatchesB = NULL,
scaNConst = 30,
scaNImp = 10,
scaNLin = 10,
scaNSig = 10,
scaMuBatchEffect = NULL,
scaSDBatchEffect = NULL,
dirOutSimulation = NULL)
## ----case-only-annotation, results='markdown'------------------------------
lsSimulatedData$dfAnnotation
## ----case-only2------------------------------------------------------------
objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = FALSE,
vecConfounders = NULL,
scaNProc = 1 )
## ----case-only-results, results='markdown'---------------------------------
head(objectImpulseDE2$dfImpulseDE2Results)
## ----case-only-batch-------------------------------------------------------
library(ImpulseDE2)
lsSimulatedData <- simulateDataSetImpulseDE2(
vecTimePointsA = rep(seq(1,8),3),
vecTimePointsB = NULL,
vecBatchesA = c(rep("B1",8), rep("B2",8), rep("B3",8)),
vecBatchesB = NULL,
scaNConst = 30,
scaNImp = 10,
scaNLin = 10,
scaNSig = 10,
scaMuBatchEffect = 1,
scaSDBatchEffect = 0.2,
dirOutSimulation = NULL)
## ----case-only-batch-annotation, results='markdown'------------------------
lsSimulatedData$dfAnnotation
## ----case-only-batch2------------------------------------------------------
objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = FALSE,
vecConfounders = c("Batch"),
scaNProc = 1 )
## ----case-only-batch-results, results='markdown'---------------------------
head(objectImpulseDE2$dfImpulseDE2Results)
## ----plot-genes------------------------------------------------------------
# Continue script of "Batch effects"
library(ggplot2)
lsgplotsGenes <- plotGenes(
vecGeneIDs = NULL,
scaNTopIDs = 10,
objectImpulseDE2 = objectImpulseDE2,
boolCaseCtrl = FALSE,
dirOut = NULL,
strFileName = NULL,
vecRefPval = NULL,
strNameRefMethod = NULL)
print(lsgplotsGenes[[1]])
## ----case-control-batch----------------------------------------------------
lsSimulatedData <- simulateDataSetImpulseDE2(
vecTimePointsA = rep(seq(1,8),3),
vecTimePointsB = rep(seq(1,8),3),
vecBatchesA = c(rep("B1",8), rep("B2",8), rep("B3",8)),
vecBatchesB = c(rep("C1",8), rep("C2",8), rep("C3",8)),
scaNConst = 30,
scaNImp = 10,
scaNLin = 10,
scaNSig = 10,
scaMuBatchEffect = 1,
scaSDBatchEffect = 0.1,
dirOutSimulation = NULL)
## ----case-control-annotation, results='markdown'---------------------------
lsSimulatedData$dfAnnotation
## ----case-control2---------------------------------------------------------
objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = TRUE,
vecConfounders = c("Batch"),
scaNProc = 1 )
## ----case-control-results, results='markdown'------------------------------
head(objectImpulseDE2$dfImpulseDE2Results)
## ----transients------------------------------------------------------------
library(ImpulseDE2)
lsSimulatedData <- simulateDataSetImpulseDE2(
vecTimePointsA = rep(seq(1,8),3),
vecTimePointsB = NULL,
vecBatchesA = c(rep("B1",8), rep("B2",8), rep("B3",8)),
vecBatchesB = NULL,
scaNConst = 0,
scaNImp = 100,
scaNLin = 0,
scaNSig = 0,
scaMuBatchEffect = 1,
scaSDBatchEffect = 0.2,
dirOutSimulation = NULL)
objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = FALSE,
vecConfounders = c("Batch"),
boolIdentifyTransients = TRUE,
scaNProc = 1 )
## ----transient-results, results='markdown'---------------------------------
head(objectImpulseDE2$dfImpulseDE2Results)
## ----heatmap---------------------------------------------------------------
# Continuing script of "Transiently regulated genes"
library(ComplexHeatmap)
lsHeatmaps <- plotHeatmap(
objectImpulseDE2 = objectImpulseDE2,
strCondition = "case",
boolIdentifyTransients = TRUE,
scaQThres = 0.01)
draw(lsHeatmaps$complexHeatmapRaw) # Heatmap based on normalised counts
## ----session---------------------------------------------------------------
sessionInfo()
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