Minor changes

lshep · Jul 18, 2017 · 57e0cda · 57e0cda
1 parent f70177e
commit 57e0cda
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,7 +5,7 @@ Authors@R: person("Lori", "Shepherd", email = "[email protected]", r
 Description: The vignette provided will have a basic sketch of the steps we
     interactively went through to build a package with devtools, version control
     with git, link to github, bioconductor advice, and submitting to bioconductor.
-Depends: R (>= 3.4.0), devtools
+Depends: R (>= 3.4.1), devtools
 License: Artistic-2.0
 Encoding: UTF-8
 LazyData: true
@@ -14,4 +14,5 @@ Suggests: knitr,
     rmarkdown,
     testthat,
     BiocStyle,
+    roxygen2
 VignetteBuilder: knitr
diff --git a/inst/doc/makeApackage.txt b/inst/doc/makeApackage.txt
@@ -123,6 +123,9 @@ http://stat545.com/packages06_foofactors-package.html
 Bioconductor Expectations 
 1. proper coding and efficient coding:
 http://bioconductor.org/developers/how-to/efficient-code/ 
+  + preallocate vectors
+  + vectorize
+  + use seq_len and seq_along instead of 1:n 1:length(n)
 http://bioconductor.org/developers/how-to/web-query/
 
 
@@ -132,7 +135,14 @@ http://bioconductor.org/developers/how-to/web-query/
      + genomic intervals - GenomicRanges Granges
      + rectangular freature x sample data - (RNAseq count matrix, microarray) - SummarizedExperiment
      + Mass Spec - MSnbase
-     + import/loading data  -  rtracklayer, GenomicAlignments, VariantAnnotation, ShortRead
+     + import/loading data  -  rtracklayer, GenomicAlignments,
+     VariantAnnotation, ShortRead
+
+     + GTF, GFF, BED, BigWig, ...	rtracklayer::import()
+     + FASTA	Biostrings::readDNAStringSet()
+     + SAM / BAM	Rsamtools::scanBam(), GenomicAlignments::readGAlignment*()
+     + VCF	VariantAnnotation::readVcf()
+     + FASTQ	ShortRead::readFastq()
      + [BiocViews](http://bioconductor.org/packages/release/BiocViews.html#___Software) 
 
 

diff --git a/vignettes/MakeAPackage.Rmd b/vignettes/MakeAPackage.Rmd
@@ -168,7 +168,7 @@ here: [rmarkdown cheetsheet](http://www.rstudio.com/wp-content/uploads/2016/03/r
      + genomic intervals - GenomicRanges Granges
      + rectangular freature x sample data - (RNAseq count matrix, microarray) - SummarizedExperiment
      + Mass Spec - MSnbase
-     + import/loading data  -  rtracklayer, GenomicAlignments, VariantAnnotation, ShortRead
+     + import/loading data  -  rtracklayer, Biostring, GenomicAlignments, VariantAnnotation, ShortRead
      + [BiocViews](http://bioconductor.org/packages/release/BiocViews.html#___Software)