Calculates a peak cutoff value given an FDR, assuming a Poisson noise
distribution estimated from the frequency of singleton and doubleton
islands.
Usage
peakCutoff(cov, fdr.cutoff = 0.001, k = 2:20)
Arguments
cov
The coverage object, e.g.,
an RleList object.
fdr.cutoff
The maximum-allowed FDR for calculating the cutoff.
k
The coverage levels at which to estimate an FDR value. The maximal
value that is less than fdr.cutoff is chosen for calculating
the cutoff. Usually best left to the default.
Value
A numeric value to use for calling peaks
Author(s)
D. Sarkar and M. Lawrence
See Also
islandDepthPlot for the graphical equivalent; the
vignette for a bit more explanation.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(chipseq)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipseq/peakCutoff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: peakCutoff
> ### Title: Calculate a peak cutoff
> ### Aliases: peakCutoff
>
> ### ** Examples
>
> data(cstest)
> cov <- coverage(resize(cstest$ctcf, width=200))
> peakCutoff(cov)
[1] 5.992367
>
>
>
>
>
> dev.off()
null device
1
>