Generics defined within ACME

Description

See methods descriptions for details.

Usage

vals(x, ...)
chromosome(object, ...)
end(x, ...)
start(x, ...)
plot(x, y, ...)
cutpoints(x, ...)
threshold(x, ...)

Arguments

Details

These are all getters for ACMESet and ACMECalcSet objects.

Value

See methods descriptions for details

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

ACMESet, ACMECalcSet

Examples

data(example.agff)
head(chromosome(example.agff))
head(end(example.agff))
head(start(example.agff))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(ACME)
Loading required package: Biobase
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

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/ACME/generics.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generics
> ### Title: Generics defined within ACME
> ### Aliases: vals chromosome threshold end plot start cutpoints
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(example.agff)
> head(chromosome(example.agff))
[1] chr1 chr1 chr1 chr1 chr1 chr1
23 Levels: chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 ... chrX
> head(end(example.agff))
[1] 18371002 18371138 18371268 18371339 18371676 18371772
> head(start(example.agff))
[1] 18370933 18371069 18371199 18371270 18371607 18371703
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>