TileCalcWinTrim {TileShuffle}R Documentation

TileCalcWinTrim

Description

Calculates arithmetic average trimmed by the minimal and maximal value on probe scores with window indices.

Usage

TileCalcWinTrim(int, win.idx)

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.

Details

Calculates arithmetic average trimmed by the minimal and maximal value 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 TileCalcWinTrim2 instead. Note that the definition of the common'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.

Value

A numeric vector containing the arithmetic mean trimmed by the minimal and maximal value of the 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]