dScale: Scaling of a vector or a dataframe.

In DepecheR: Determination of essential phenotypic elements of clusters in high-dimensional entities

Description

This is a scaling function with a number of alternatives. This method for scaling takes the shape of the data into somewhat more of a consideration than minMaxScale does, but still gives less influence of outliers than more conventional scalin alternatives, such as unit variance scaling.

Usage

dScale(
  x,
  control,
  scale = TRUE,
  robustVarScale = TRUE,
  center = "peak",
  truncate = FALSE,
  multiplicationFactor = 1,
  returnCenter = FALSE,
  nCores = "default"
)

Arguments

x	A numeric/integer vector or dataframe
control	A numeric/integer vector or dataframe of values that could be used to define the range. If no control data is present, the function defaults to using the indata as control data.
scale	If scaling should be performed. Three possible values: a vector with two values indicating the low and high threshold quantiles for the scaling, TRUE, which equals the vector 'c(0.001, 0.999)', and FALSE.
robustVarScale	If the data should be scaled to its standard deviation within the quantiles defined by the scale values above. If TRUE (the default), the data is unit variance scaled based on the standard deviation of the data within the range defined by scale.
center	If centering should be performed. Alternatives are mean', 'peak' and FALSE. 'peak' results in centering around the highest peak in the data, which is useful in most cytometry situations. 'mean' results in mean centering.
truncate	If truncation of the most extreme values should be performed. Three possible values: TRUE, FALSE, and a vector with two values indicating the low and high threshold quantiles for truncation.
multiplicationFactor	A value that all values will be multiplied with. Useful e.g. if the results preferrably should be returned as percent. Defaults to FALSE.
returnCenter	Boolean. If center=TRUE, should the value at the center be returned?
nCores	If the function is run in multicore mode, which it will if the dataset is large (nrow*ncol>10^6), this decides the number of cores. The default is currently 87.5 percent with a cap on 10 cores, as no speed increase is generally seen above 10 cores for normal computers to date.

Value

A vector or dataframe with the same size but where all values in the vector or column of the dataframe have been internally scaled. In addition, if returnCenter=TRUE, a value, or a vector if x is a matrix or a data frame.

Examples

# Load some data
data(testData)

# Retrieve the first column
x <- testData[, 2]

# The maximum and minimum values are
max(x)
min(x)

# Run the function without mean centering and with the quantiles set to 0
# and 1.
y <- dScale(x, scale = c(0, 1), robustVarScale = FALSE, center = FALSE)

# And the data has been scaled to the range between 0 and 1.
max(y)
min(y)

# Now run the default function for a dataframe
summary(testData[, 2:15])

y_df <- dScale(testData[, 2:15])

# Here, the data has first been truncated to the default percentiles, then
# scaled to the standard deviation in the remaining interval and finally the
# center has been placed where the highest peak in the data is present.
# NB! Here, no truncation has been performed in the scaling, only to obtain
# the scaling values.

summary(y_df)

DepecheR documentation built on Nov. 8, 2020, 5:44 p.m.