biosigner-vignette.R
In biosigner: Signature discovery from omics data

## ----global_options, include=FALSE--------------------------------------------
knitr::opts_chunk$set(fig.width = 6, fig.height = 6, fig.path = 'figures/')

## ----loading, message = FALSE-------------------------------------------------
library(biosigner)

## ----diaplasma----------------------------------------------------------------
data(diaplasma)

## ----diaplasma_strF-----------------------------------------------------------
attach(diaplasma)
library(ropls)
ropls::view(dataMatrix)
ropls::view(sampleMetadata, standardizeL = TRUE)
ropls::view(variableMetadata, standardizeL = TRUE)

## ----diaplasma_plot-----------------------------------------------------------
with(sampleMetadata,
plot(age, bmi, cex = 1.5, col = ifelse(type == "T1", "blue", "red"), pch = 16))
legend("topleft", cex = 1.5, legend = paste0("T", 1:2),
text.col = c("blue", "red"))

## ----select-------------------------------------------------------------------
featureSelVl <- variableMetadata[, "mzmed"] >= 450 &
variableMetadata[, "mzmed"] < 500
sum(featureSelVl)
dataMatrix <- dataMatrix[, featureSelVl]
variableMetadata <- variableMetadata[featureSelVl, ]

## ----biosign------------------------------------------------------------------
diaSign <- biosigner::biosign(dataMatrix, sampleMetadata[, "type"], bootI = 5)

## ----boxplot------------------------------------------------------------------
biosigner::plot(diaSign, typeC = "boxplot")

## ----signature----------------------------------------------------------------
variableMetadata[getSignatureLs(diaSign)[["complete"]], ]

## ----train--------------------------------------------------------------------
trainVi <- 1:floor(0.8 * nrow(dataMatrix))
testVi <- setdiff(1:nrow(dataMatrix), trainVi)

## ----biosign_train, warning = FALSE-------------------------------------------
diaTrain <- biosigner::biosign(dataMatrix[trainVi, ], sampleMetadata[trainVi, "type"],
bootI = 5)

## ----predict------------------------------------------------------------------
diaFitDF <- biosigner::predict(diaTrain)

## ----confusion----------------------------------------------------------------
lapply(diaFitDF, function(predFc) table(actual = sampleMetadata[trainVi,
"type"], predicted = predFc))

## ----accuracy-----------------------------------------------------------------
sapply(diaFitDF, function(predFc) {
conf <- table(sampleMetadata[trainVi, "type"], predFc)
conf <- sweep(conf, 1, rowSums(conf), "/")
round(mean(diag(conf)), 3)
})

## ----getAccuracy--------------------------------------------------------------
round(biosigner::getAccuracyMN(diaTrain)["S", ], 3)

## ----performance--------------------------------------------------------------
diaTestDF <- biosigner::predict(diaTrain, newdata = dataMatrix[testVi, ])
sapply(diaTestDF, function(predFc) {
conf <- table(sampleMetadata[testVi, "type"], predFc)
conf <- sweep(conf, 1, rowSums(conf), "/")
round(mean(diag(conf)), 3)
})

## ----expressionset_code, warning = FALSE, message = FALSE---------------------
library(Biobase)

diaSet <- Biobase::ExpressionSet(assayData = t(dataMatrix),
                                 phenoData = new("AnnotatedDataFrame",
                                                 data = sampleMetadata),
                                 featureData = new("AnnotatedDataFrame",
                                                 data = variableMetadata))

ropls::view(diaSet)

biosigner::biosign(diaSet, "type", bootI = 5)

## ----view_ExpressionSet-------------------------------------------------------
ropls::view(diaSet)

## ----detach-------------------------------------------------------------------
detach(diaplasma)

## ----sacurine-----------------------------------------------------------------
data(sacurine)
sacSign <- biosigner::biosign(sacurine[["dataMatrix"]],
sacurine[["sampleMetadata"]][, "gender"],
methodVc = "plsda")

## ----biomark, warning = FALSE, message = FALSE--------------------------------
library(BioMark)
data(SpikePos)
group1Vi <- which(SpikePos[["classes"]] %in% c("control", "group1"))
appleMN <- SpikePos[["data"]][group1Vi, ]
spikeFc <- factor(SpikePos[["classes"]][group1Vi])
annotDF <- SpikePos[["annotation"]]
rownames(annotDF) <- colnames(appleMN)

## ----biomark_pca--------------------------------------------------------------
biomark.pca <- ropls::opls(appleMN, fig.pdfC = "none")
ropls::plot(biomark.pca, parAsColFcVn = spikeFc)

## ----biomark_pls--------------------------------------------------------------
biomark.pls <- ropls::opls(appleMN, spikeFc)

## ----apple_biosign, warning = FALSE-------------------------------------------
appleSign <- biosigner::biosign(appleMN, spikeFc)

## ----annotation---------------------------------------------------------------
annotDF <- SpikePos[["annotation"]]
rownames(annotDF) <- colnames(appleMN)
annotDF[getSignatureLs(appleSign)[["complete"]], c("adduct", "found.in.standards")]

## ----golub_false, warning = FALSE, message = FALSE----------------------------
library(golubEsets)
data(Golub_Merge)
golubMN <- t(exprs(Golub_Merge))
leukemiaFc <- pData(Golub_Merge)[["ALL.AML"]]
table(leukemiaFc)
varSubVi <- 1501:2000
golubSign <- biosigner::biosign(golubMN[, varSubVi], leukemiaFc, methodVc = "svm")

## ----hu6800, warning = FALSE, message = FALSE---------------------------------
library(hu6800.db)
sapply(biosigner::getSignatureLs(golubSign)[["complete"]],
       function(probeC)
       get(probeC, env = hu6800GENENAME))

## ----empty, echo = FALSE------------------------------------------------------
rm(list = ls())

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()