R: Compute summaries for cumulative subsets of a short-read data...
subsetSummary
R Documentation
Compute summaries for cumulative subsets of a short-read data set.
Description
THIS FUNCTION IS DEFUNCT!
Divides a short-read dataset into several subsets, and computes
various summaries cumulatively. The goal is to study the
characteristics of the data as a function of sample size.
A "GRanges" object representing alignment
locations at the sample level.
chr
The chromosome for which the summaries are to be obtained.
Must specify a valid element of x
nstep
The number of maps in each increment for the full
dataset (not per-chromosome). This will be translated to a
per-chromosome number proportionally.
props
Alternatively, an increasing sequence of proportions
determining the size of each subset. Overrides nstep.
chromlens
A named vector of per-chromosome lengths, typically
the result of seqlengths.
fg.cutoff
The coverage depth above which a region would be
considered foreground.
seqLen
The number of bases to which to extend each read before
computing coverage.
resample
Logical; whether to randomly reorder the reads before
dividing them up into subsets. Useful to remove potential order
effects (for example, if data from two lanes were combined to
produce x).
fdr.cutoff
The maximum false discovery rate for a region that
is considered to be foreground.
use.fdr
Whether to use the FDR detected peaks when calling
foreground and background.
islands
Logical. If TRUE, the whole island would be
considered foreground if the maximum depth equals or exceeds
fg.cutoff. If FALSE, only the region above the cutoff
would be considered foreground.
verbose
logical controlling whether progress information will
be shown during computation (which is potentially long-running).
Value
A data frame with various per-subset summaries.
Note
This function should be considered preliminary, in that it might
change significantly or simply be removed in a subsequent version.
If you like it the way it is, please notify the maintainer.