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Last data update: 2014.03.03

R: Read Nimblegen GFF files

read.resultsGFF

R Documentation

Read Nimblegen GFF files

Description

A GFF format file is a quite flexible format for storing genomic data. Nimblegen uses these format files as one format for making chip-chip data available. This function reads these files, one per experiment and creates a resulting aGFF-class object.

Usage

read.resultsGFF(fnames, path = ".", samples = NULL, notes = NULL, skip = 0, sep = "\t", quote = """, ...)

Arguments

`fnames`	A vector of filenames
`path`	The path to the filenames
`samples`	A data.frame containing sample information, one row per sample, in the same order as the files in fnames
`notes`	A character vector for notes–not currently stored
`skip`	Number of lines to skip if the file contains a header
`sep`	The field separator–should be a tab character for gff files, but can be set if necessary.
`quote`	The text quote character–again not used for gff file, typically
`...`	...

Details

The output is an ACMESet object.

Value

A single ACMESet object.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

References

http://www.sanger.ac.uk/Software/formats/GFF/

Examples

datdir <- system.file('extdata',package='ACME')
fnames <- dir(datdir)
example.agff <- read.resultsGFF(fnames,path=datdir)

Results


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)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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(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/read.resultsGFF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: read.resultsGFF
> ### Title: Read Nimblegen GFF files
> ### Aliases: read.resultsGFF
> ### Keywords: IO manip
> 
> ### ** Examples
> 
> datdir <- system.file('extdata',package='ACME')
> fnames <- dir(datdir)
> example.agff <- read.resultsGFF(fnames,path=datdir)
[1] "Reading /home/ddbj/local/lib64/R/library/ACME/extdata/testsamp1.gff"
[1] "Reading /home/ddbj/local/lib64/R/library/ACME/extdata/testsamp2.gff"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>