TileDivideByGC {TileShuffle}R Documentation

TileDivideByGC

Description

Automatically creates GC content bins.

Usage

TileDivideByGC(gc, gcnum=3)

Arguments

gc A numeric vector containing the GC content of each probe.
gcnum The number of preferred GC content bins that should be automatically created. Note that if gcnum is higher than the available number of different GC content values, it will be set to this maximal number (including a warning message).

Details

Automatically creates GC content bins under given number of bins. In order to maintain sufficiently large permutation sizes for each GC content bin, the method tries to balance the number of probes within each bin. More precisely, initially a bin is created for each GC content value and iteratively two neighboring bins are merged if their combined number of probes is minimal among all possible neighboring bins. The procedure stops if the given number of gcnum is reached. In such a way, the most balanced bin sizes can be obtained with the given distribution of GC content values. The method returns

Value

A vector with the bin boundaries b. The ith bin contains all probes with a GC content within the range [b[i], b[i+1]).


[Package TileShuffle version 0.1.0 Index]