TileCalcScr {TileShuffle}R Documentation

TileCalcScr

Description

Calculates scores using different functions.

Usage

TileCalcScr(int, score.function=c("mean", "trimmed", "median"))

Arguments

int A numeric vector of one or more intensities or fold changes. It may contain NA values that are excluded from the calculation.
score.function Function to calculate windows scores over the log2-intensities or log2-fold changes of the corresponding probes, i.e., arithmetic average (score.function = "mean"), arithmetic mean trimmed by the minimal and maximal value (score.function = "trimmed"), or the median (score.function = "median"). Note that the definition of trimmed mean differs from the common one with given percentile ranges. Moreover, the resulting scores with trimmed mean may only differ from the mean only in case of windows that contain more than two probes. The latter two scoring functions are recommended due to their higher robustness against outliers. However, due to the higher calculation costs, the running time increases by selecting "trimmed" or "median". Note that the function is given as character.

Details

Calculates scores using different functions on probe scores.

Value

Returns the calculated value with the selected scoring functions. Note that windows of length zero are reported with a window score of NA. Moreover, probe scores with the value NA are excluded from the calculation.


[Package TileShuffle version 0.1.0 Index]