Browse code

export and document cmetindex command

Michael Lawrence authored on 14/11/2017 22:43:33
Showing2 changed files

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@@ -34,7 +34,7 @@ importMethodsFrom(GenomicAlignments, qwidth)
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 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
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        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
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        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,
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-       GmapParam)
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+       GmapParam, cmetindex)
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 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
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               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
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new file mode 100644
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@@ -0,0 +1,34 @@
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+\name{cmetindex}
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+\alias{cmetindex}
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+\title{
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+  Call the cmetindex command
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+}
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+\description{
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+  Call the GMAP \command{cmetindex} command to build an index suitable
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+  for alignment of bisulfite-treated DNA, by allowing for C->T and G->A
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+  differences.
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+
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+}
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+\usage{
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+cmetindex(db, use_snps = NULL)
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+}
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+%- maybe also 'usage' for other objects documented here.
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+\arguments{
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+  \item{db}{
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+    The GmapGenome object
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+  }
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+  \item{use_snps}{
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+    A GmapSnps object for generating a SNP-tolerant index
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+  }
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+}
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+\author{
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+  Michael Lawrence
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+}
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+
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+\examples{
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+\dontrun{
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+    library(BSgenome.Dmelanogaster.UCSC.dm3)
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+    flyGG <- GmapGenome(Dmelanogaster, create = TRUE)
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+    cmetindex(flyGG)
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+}
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+}