Get the refflat table from ucsc for the given genome

Description

Fetches the refflat table from ucsc, stores in temp dir and then gunzips it and reads it in.

Usage

getRefflat(genome = "hg17")

Arguments

Value

A data frame mirroring the UCSC table structure.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

References

http://genome.ucsc.edu

See Also

findClosestGene

Examples

rf <- getRefflat('hg17')

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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> 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/getRefflat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getRefflat
> ### Title: Get the refflat table from ucsc for the given genome
> ### Aliases: getRefflat
> ### Keywords: IO
> 
> ### ** Examples
> 
> rf <- getRefflat('hg17')
trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/refFlat.txt.gz'
Content type 'application/x-gzip' length 3423284 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  seek on a gzfile connection returned an internal error
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>