TileCalcWinScr {TileShuffle}R Documentation

TileCalcWinScr

Description

Wrapper function for calculating window scores using different functions with window indices.

Usage

TileCalcWinScr(int, win.idx, 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.idx A list with the maximal number of probes in a window as its length. In entry i, it stores only start positions of windows containing at least (i+1) probes.
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 window indices, a list storing window start positions. More precisely, win.idx has the maximal number of probes in a window as length and in its ith entry, it stores only start positions of windows containing at least (i+1) probes. In case of short but numerous windows, the window scores can be calculated very efficiently by use of optimized vector operations. Otherwise, please consider using TileCalcWinScr2 instead.

Value

A numeric vector containing the calculated window scores for each possible start position. Note that windows of length zero are not supported and hence treated as windows of length one. Moreover, probe scores with the value NA are excluded from the calculation.


[Package TileShuffle version 0.1.0 Index]