Here are my changes to your code

[scoetzee]

Also think about removing your ReadBed and ReadGFF functions.

There are built in functions in bioconductor from the rtracklayer package

[scoetzee]

BiocCheck out

• This is BiocCheck, version 1.2.3.
• BiocCheck is a work in progress. Output and severity of issues may change.
• Installing package...
  • CONSIDER: Clarifying how objects TRUESS.range, TRUEFs, TRUEF.meth.cor, TRUERange, upperOR, lowerOR (used in get.feature.probe, get.TFs, GetNearGenes, motif.enrichment.plot, scatter, TF.rank.plot) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within().
• Unknown package type, checking vignette directories...
  • REQUIRED: 'vignettes' directory!
• Checking version number...
  • REQUIRED: Valid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/
• Checking biocViews...
  • REQUIRED: Add some biocViews!
• Checking build system compatibility...
  • REQUIRED: Authors@R must evaluate to 'person' object!
• Checking unit tests...
  • CONSIDER: Adding unit tests. We strongly recommend them. See http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/.
• Checking native routine registration...
• Checking for deprecated package usage...
• Parsing R code in R directory, examples, vignettes...
• Checking for T...
• Checking for F...
• Checking for browser()...
• Checking for <<-...
• Checking for library/require of ELMER...
• Checking DESCRIPTION/NAMESPACE consistency...
• Checking function lengths..............
• The longest function is 208 lines long
• The longest 5 functions are:
• TCGA.pipe() (R/TCGA_pipe.R, line 16): 208 lines
• fetch.mee() (R/Small.R, line 86): 98 lines
• NearGenes() (R/GetNearbyGenes.R, line 10): 96 lines
• schematic() (R/Schematic.plot.R, line 102): 96 lines
• get.TFs() (R/Main_function.R, line 403): 81 lines
• Checking man pages...
  • RECOMMENDED: Add non-empty \value sections to the following man pages: get450K.Rd, getClinic.Rd, getExp.Rd, getGeneInfo.Rd, getMeth.Rd, getPair.Rd, getProbeInfo.Rd, getRNAseq.Rd, getSample.Rd, getTCGA.Rd, matrixClinic.Rd, matrixMeth.Rd, matrixRNA.Rd, motif.enrichment.plot.Rd, schematic.Rd, splitmatrix.Rd, Stat.diff.meth.Rd, TF.rank.plot.Rd
• Checking exported objects have runnable examples...
  • REQUIRED: At least 80% of man pages documenting exported objects must have runnable examples.The following pages do not: fetch.mee.Rd, fetch.pair.Rd, get.diff.meth.Rd, get.enriched.motif.Rd, get.pair.Rd, get.permu.Rd, get.TFs.Rd, getExp.Rd, getGeneID.Rd, getGeneInfo.Rd, getMeth.Rd, GetNearGenes.Rd, getPair.Rd, getProbeInfo.Rd, getSample.Rd, getSymbol.Rd, getTCGA.Rd, motif.enrichment.plot.Rd, ReadBed.Rd, ReadGFF.Rd, scatter.plot.Rd, schematic.plot.Rd, TCGA.pipe.Rd, TF.rank.plot.Rd, WriteBed.Rd
• Checking package NEWS...
  • CONSIDER: Adding a NEWS file, so your package news will be included in Bioconductor release announcements.
• Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source...
  • CONSIDER: Shortening lines; 293 lines (7%) are > 80 characters long.
  • CONSIDER: Replacing tabs with 4 spaces; 82 lines (1%) contain tabs.
  • CONSIDER: Indenting lines with a multiple of 4 spaces; 1204 lines (29%) are not. See http://bioconductor.org/developers/how-to/coding-style/
• Checking for canned comments in man pages...

Summary: REQUIRED count: 5 RECOMMENDED count: 1 CONSIDERATION count: 6 For detailed information about these checks, see the BiocCheck vignette, available at http://www.bioconductor.org/packages/3.0/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output BiocCheck FAILED. $requirements [1] "'vignettes' directory!" [2] "Valid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/" [3] "Add some biocViews!" [4] "Authors@R must evaluate to 'person' object!" [5] "At least 80% of man pages documenting exported objects must have runnable examples.The following pages do not:"

$recommendations [1] "Add non-empty \value sections to the following man pages:"

$considerations [1] "Clarifying how objects TRUESS.range, TRUEFs, TRUEF.meth.cor, TRUERange, upperOR, lowerOR (used in get.feature.probe, get.TFs, GetNearGenes, motif.enrichment.plot, scatter, TF.rank.plot) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within()." [2] "Adding unit tests.\n We strongly recommend them. See\n http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/." [3] "Adding a NEWS file, so your package news will be included in Bioconductor release announcements." [4] "Shortening lines; 293 lines (7%) are > 80 characters long." [5] "Replacing tabs with 4 spaces; 82 lines (1%) contain tabs." [6] "Indenting lines with a multiple of 4 spaces; 1204 lines (29%) are not."