vignettes/MethPed-vignette.R

In mashranga/MethPed: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

## ------------------------------------------------------------------------
## Data Structure

## ---- include=FALSE------------------------------------------------------
## Data Structure
library(MethPed)
data(MethPed_sample)
MethPed_sample_v1<- MethPed_sample

## ---- echo=FALSE---------------------------------------------------------
head(MethPed_sample_v1)

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## Data class

## ---- echo=FALSE---------------------------------------------------------
class(MethPed_sample_v1)

## ---- include=FALSE------------------------------------------------------
library(Biobase)

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## Data Structure

## ---- echo=FALSE---------------------------------------------------------
MethPed_sample_v2<-Biobase::exprs(MethPed_sample)
head(MethPed_sample_v2)

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## Data class

## ---- echo=FALSE---------------------------------------------------------
class(MethPed_sample_v2)

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## Data Structure

## ---- echo=FALSE---------------------------------------------------------
MethPed_sample_v3 <- data.frame(MethPed_sample_v2)
MethPed_sample_v3$TargetID <- rownames(MethPed_sample_v3)
rownames(MethPed_sample_v3) <-NULL
head(MethPed_sample_v3)

## ------------------------------------------------------------------------
## Data class

## ---- echo=FALSE---------------------------------------------------------
class(MethPed_sample_v3)

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# List of 900 probes in predictors
library(MethPed)
data(MethPed_900probes)
head(MethPed_900probes)

## ----Loading_package_and_data--------------------------------------------
# Loading package
library(MethPed)
# Loading data set
data(MethPed_sample)
head(MethPed_sample)
class(MethPed_sample)

## ----Check_missing_probe_data, echo=TRUE---------------------------------
## Check for missing value 
missingIndex <- checkNA(MethPed_sample)
missingIndex

## ---- include=FALSE------------------------------------------------------
set.seed(1000)

## ----Run_MethPed_classifier, echo=TRUE, message=TRUE, warning=FALSE------
# Run the MethPed classifier
myClassification <- MethPed(MethPed_sample)

## ----Output_of_Methped_classifier----------------------------------------
myClassification

## ----MethPed_classifier_output_description_1-3---------------------------
# First part
myClassification$target_id
# Second part
myClassification$probes
# Third part
myClassification$sample

## ----MethPed_classifier_output_description_4-----------------------------
# Fourth part
myClassification$probes_missing

## ----MethPed_classifier_output_description_5-----------------------------
# Fifth part
myClassification$oob_err.rate

## ----MethPed_classifier_output_description_6-----------------------------
# Sixth part
myClassification$predictions

## ----Summary_of_MethPed_classifier_1-------------------------------------
summary(myClassification)

## ---- include=FALSE------------------------------------------------------
set.seed(1000)

## ---- include=FALSE------------------------------------------------------
myClassification_max <- MethPed(MethPed_sample,prob=FALSE)

## ---- echo=FALSE---------------------------------------------------------
summary(myClassification_max)

## ----MethPed_bar_plot_custom_code----------------------------------------
par(mai = c(1, 1, 1, 2), xpd=TRUE)
mat<-t(myClassification$predictions)
mycols <- c("green",rainbow(nrow(mat),start=0,end=1)[nrow(mat):1],"red")
barplot(mat,  col = mycols,
                beside=FALSE,axisnames=TRUE,
                ylim=c(0,1),xlab= "Sample",ylab="Probability")
legend( ncol(mat)+0.5,1,
          legend = rownames(mat),fill = mycols,xpd=TRUE, cex = 0.6)

## ----MethPed_bar_plot_generic_function_TRUE, echo=FALSE------------------
plot(myClassification)

## ----MethPed_bar_plot_generic_function_FALSE, echo=FALSE-----------------
plot(myClassification_max)

## ----Function_to_get_missing_probes--------------------------------------
probeMis(myClassification)

## ------------------------------------------------------------------------
# Loading dataset
data(MethPed_sample)
class(MethPed_sample)

## ---- include=FALSE------------------------------------------------------
library(Biobase)

## ---- echo=FALSE---------------------------------------------------------
MethPed_sample_matrix<-Biobase::exprs(MethPed_sample)
head(MethPed_sample_matrix)

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class(MethPed_sample_matrix)

## ------------------------------------------------------------------------
checkNA(MethPed_sample_matrix)

## ------------------------------------------------------------------------
MethPed_sample_missing<-MethPed_sample_matrix
MethPed_sample_missing[c(1,10,200),2]<-NA
MethPed_sample_missing[c(4,600,500,1000),1]<-NA
head(MethPed_sample_missing,10)

## ------------------------------------------------------------------------
checkNA(MethPed_sample_missing)

## ----Delete_random_seed--------------------------------------------------
if(exists(".Random.seed")) rm(.Random.seed)

## ---- include=FALSE------------------------------------------------------
library(impute)
imputedData <- impute.knn(MethPed_sample_missing)

## ----Combine_probe_name_with_impoted_data, include=FALSE-----------------
imputedData <- imputedData$data

## ---- echo=FALSE---------------------------------------------------------
checkNA(imputedData)

## ---- include=FALSE------------------------------------------------------
set.seed(1000)

## ---- include=FALSE------------------------------------------------------
myClassification <- MethPed(imputedData)

## ---- echo=FALSE---------------------------------------------------------
summary(myClassification)

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citation('MethPed')

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sessionInfo()