TileCalcWinGC {TileShuffle}R Documentation

TileCalcWinGC

Description

Calculates the average GC content with window indices.

Usage

TileCalcWinGC(gc, win.idx)

Arguments

gc A numeric vector containing the GC content of one or more probes. The GC content is the sum of the relative numbers of Cs and Gs in the probe sequence.
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 the average window GC content on probe GC contents with window indices, 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 average GC content in windows can be calculated very efficiently by use of optimized vector operations. Otherwise, please consider using TileCalcWinGC2 instead.

Value

A numeric vector containing the average GC content per window. Note that windows of length zero are not supported and hence treated as windows of length one. Moreover, GC content with the value NA are excluded from the calculation.


[Package TileShuffle version 0.1.0 Index]