Last data update: 2014.03.03

R: Load HMMs from files
loadHmmsFromFilesR Documentation

Load HMMs from files

Description

Load aneuHMM objects from file into a list.

Usage

loadHmmsFromFiles(hmms, strict = TRUE)

Arguments

hmms

A list of files that contain aneuHMM objects.

strict

If any of the loaded objects is not a aneuHMM object, an error (strict=TRUE) or a warning (strict=FALSE) will be generated.

Value

A list() containing all loaded aneuHMM objects.

Author(s)

Aaron Taudt

Examples

## Get some files that you want to load
folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
files <- list.files(folder, full.names=TRUE)
## Load and plot the first then
hmms <- loadHmmsFromFiles(files[1:10])
lapply(hmms, plot, type='profile')

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(AneuFinder)
Loading required package: GenomicRanges
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: GenomeInfoDb
Loading required package: cowplot
Loading required package: ggplot2

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

Loading required package: AneuFinderData
Loading AneuFinder
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AneuFinder/loadHmmsFromFiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadHmmsFromFiles
> ### Title: Load HMMs from files
> ### Aliases: loadHmmsFromFiles
> 
> ### ** Examples
> 
> ## Get some files that you want to load
> folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
> files <- list.files(folder, full.names=TRUE)
> ## Load and plot the first then
> hmms <- loadHmmsFromFiles(files[1:10])
Loading univariate HMMs from files ... 0.02s
> lapply(hmms, plot, type='profile')
transforming coordinates ... 0.16s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
transforming coordinates ... 0s
$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_001.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_002.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_003.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_004.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_005.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_006.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_007.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_008.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_009.bam`

$`/home/ddbj/local/lib64/R/library/AneuFinderData/extdata/primary-lung/hmms/AvdB150303_I_010.bam`

> 
> 
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> 
> dev.off()
null device 
          1 
>