r-rsc-statistics-data-mining/outlier-detection.R at master · sing-group/r-rsc-statistics-data-mining · GitHub

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source("load-cancer.R")

#	---------------------------------------------------------------------------
#
#	1. Outlier detection
#
#	---------------------------------------------------------------------------

# The spectra length is the number of peaks that it holds.
spectraLengths <- sapply(data$spectra, length)


# Calculate the mean intensity of the peaks in the spectra.
intensityMeans <-
  sapply(data$spectra, function(spectra)
    mean(intensity(spectra)))


# Data is grouped in a data frame, so that it can be used in the boxplot function.
dataFrame <- data.frame(
  "spectra" = data$spectraNames,
  "samples" = data$sampleNames,
  "spectraLengths" = spectraLengths,
  "intensityMeans" = intensityMeans,
  stringsAsFactors = FALSE
)

# This graphical configuration allows including two plots in the same window.
par(mfrow = c(1, 2))

# Generation of the boxplot for the spectra lengths.
bpLength = boxplot(
  spectraLengths ~ samples,
  data = dataFrame,
  main = "Spectra Size",
  ylab = "Number of peaks",
  xlab = "Sample",
  col = data$samplesColors
)


# Generation of the boxplot for the mean peak intensity.
bpIntensity = boxplot(
  intensityMeans ~ samples,
  data = dataFrame,
  main = "Intensities",
  ylab = "Mean Intensity",
  xlab = "Sample",
  col = data$samplesColors
)

# The boxplot result includes the "out" attribute, a vector with the outlier values.
# The spectra with outlier values in the characteristics analyzed are extracted here.
dataFrame[dataFrame$spectraLengths %in% bpLength$out, ]
dataFrame[dataFrame$intensityMeans %in% bpIntensity$out, ]

#	---------------------------------------------------------------------------
#
#	2. Spectra comparison
#
#	---------------------------------------------------------------------------

source("multiple-sample-visualization-functions.R")

par(mfrow = c(2, 2))
compareSpectra(data$spectra[[7]], data$spectra[[6]])
compareSpectra(data$spectra[[7]], data$spectra[[8]])
compareSpectra(data$spectra[[7]], data$spectra[[9]])
compareSpectra(data$spectra[[7]], data$spectra[[10]])