subsetSummary {chipseq} | R Documentation |
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.
subsetSummary(x, chr, nstep, props = seq(0.1, 1, 0.1), chromlens = seqlengths(x), fg.cutoff = 6, seqLen = 200, fdr.cutoff = 0.001, use.fdr = FALSE, resample = TRUE, islands = TRUE, verbose = getOption("verbose"))
x |
A |
chr |
The chromosome for which the summaries are to be obtained.
Must specify a valid element of |
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 |
chromlens |
A named vector of per-chromosome lengths, typically
the result of |
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 |
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 |
verbose |
logical controlling whether progress information will be shown during computation (which is potentially long-running). |
A data frame with various per-subset summaries.
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.
Deepayan Sarkar, Michael Lawrence