Nothing
## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"--------------------
BiocStyle::latex()
## ----setup, echo=FALSE-----------------------------------------------------
knitr::opts_chunk$set(message=FALSE, fig.align="center", comment="")
## ----echo=FALSE------------------------------------------------------------
x <- citation("missRows")
## ----eval=FALSE------------------------------------------------------------
# help("MIMFA")
## ----eval=FALSE------------------------------------------------------------
# ?MIMFA
## ----quickStart, eval=FALSE------------------------------------------------
# ## Data preparation
# midt <- MIDTList(table1, table2, colData=df)
#
# ## Performing MI
# midt <- MIMFA(midt, ncomp=2, M=30)
#
# ## Analysis of the results - Visualization
# plotInd(midt)
# plotVar(midt)
## ----eval=FALSE------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
# install.packages("BiocManager")
# BiocManager::install()
## ----install, eval=FALSE---------------------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
# install.packages("BiocManager")
# BiocManager::install("missRows")
## ----loadLibrary, message=FALSE, warning=FALSE-----------------------------
library(missRows)
## ----searchHelp, eval=FALSE------------------------------------------------
# help.search("missRows")
## ----loadData--------------------------------------------------------------
data(NCI60)
## --------------------------------------------------------------------------
names(NCI60)
## --------------------------------------------------------------------------
table(NCI60$dataTables$cell.line$type)
## --------------------------------------------------------------------------
NCI60$mae
## --------------------------------------------------------------------------
data(NCI60)
## ----dirMIDTList-----------------------------------------------------------
tableList <- NCI60$dataTables[1:2]
cell.line <- NCI60$dataTables$cell.line
midt <- MIDTList(tableList, colData=cell.line,
assayNames=c("trans", "prote"))
## ----sepMIDTList-----------------------------------------------------------
table1 <- NCI60$dataTables$trans
table2 <- NCI60$dataTables$prote
cell.line <- NCI60$dataTables$cell.line
midt <- MIDTList(table1, table2, colData=cell.line,
assayNames=c("trans", "prote"))
## ----sepMIDTList2----------------------------------------------------------
midt <- MIDTList("trans" = table1, "prote" = table2,
colData=cell.line)
## ----maeMIDTList-----------------------------------------------------------
midt <- MIDTList(NCI60$mae)
## --------------------------------------------------------------------------
midt
## ----MIMFA, echo=2---------------------------------------------------------
set.seed(123)
midt <- MIMFA(midt, ncomp=50, M=30, estimeNC=TRUE)
## --------------------------------------------------------------------------
midt
## --------------------------------------------------------------------------
names(midt)
## --------------------------------------------------------------------------
cell.line <- colData(midt)
## ----MthConf---------------------------------------------------------------
conf <- configurations(midt, M=5)
dim(conf)
## ----missingPattern, fig.width=6, fig.height=5, out.width="0.6\\textwidth"----
patt <- missPattern(midt, colMissing="grey70")
## ----missingPatternMat-----------------------------------------------------
patt
## ----plotInd, fig.width=6, fig.height=5, out.width="0.55\\textwidth"-------
plotInd(midt, colMissing="white")
## ----plotInd-ellipses, fig.width=6, fig.height=5, out.width="0.55\\textwidth"----
plotInd(midt, confAreas="ellipse", confLevel=0.95)
## ----plotInd-convexhull, fig.width=6, fig.height=5, out.width="0.55\\textwidth"----
plotInd(midt, confAreas="convex.hull")
## ----plotVar, fig.width=6, fig.height=5, out.width="0.55\\textwidth"-------
plotVar(midt, radIn=0.5)
## ----plotVar-cutoff, fig.width=6, fig.height=5, out.width="0.55\\textwidth"----
plotVar(midt, radIn=0.55, varNames=TRUE, cutoff=0.55)
## ----tuneM, echo=FALSE-----------------------------------------------------
set.seed(1)
tune <- tuneM(midt, ncomp=2, Mmax=100, inc=10, N=20, showPlot=FALSE)
## ----eval=FALSE------------------------------------------------------------
# tune <- tuneM(midt, ncomp=2, Mmax=100, inc=10, N=20)
# tune
## --------------------------------------------------------------------------
tune$stats
## ----echo=FALSE, fig.width=6.5, fig.height=5, out.width="0.5\\textwidth"----
tune$ggp
## ----session-info, echo=FALSE----------------------------------------------
sessionInfo()
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