TileCalcWinScr2 {TileShuffle}R Documentation

TileCalcWinScr2

Description

Wrapper function for calculating window scores using different functions.

Usage

TileCalcWinScr2(int, win.st, win.len, score.function=c("mean",
    "trimmed", "median"))

Arguments

int A numeric vector containing one or more probe scores (i.e. intensities or log-fold changes).
win.st An integer vector containing one or more window start positions in int.
win.len An integer vector containing one or more window lengths. It must be of same length as win.st.
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

Wrapper function for calculating window scores using different functions on probe scores with given start positions and window lengths. In case of few but longer windows, this function is superior to TileCalcWinScr which is optimized for short windows.

Value

A numeric vector containing the calculated window scores for the given start positions. 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]