inst/doc/genbankr.R

## --------------------------------------------------------------------------
suppressPackageStartupMessages(library(genbankr))
smpfile = system.file("sample.gbk", package="genbankr")
gb = readGenBank(smpfile)
gb

## --------------------------------------------------------------------------
genes(gb)

## ---- results='hide'-------------------------------------------------------
cds(gb)
exons(gb)
transcripts(gb)

## ---- results='hide'-------------------------------------------------------
variants(gb)
otherFeatures(gb)


## --------------------------------------------------------------------------
accession(gb)
vers(gb)

## --------------------------------------------------------------------------
seqinfo(gb)

## --------------------------------------------------------------------------
getSeq(gb)

## --------------------------------------------------------------------------
pg = parseGenBank(smpfile)
str(pg, max.level = 1)

## --------------------------------------------------------------------------
gbf = readGenBank(smpfile, ret.seq = FALSE)
gbf

## --------------------------------------------------------------------------
gbkfile = GenBankFile(smpfile)
gb2 = import(gbkfile)

## --------------------------------------------------------------------------
gba = GBAccession("U49845.1")
gba

## --------------------------------------------------------------------------
readGenBank(gba, partial=TRUE)

## --------------------------------------------------------------------------
getSeq(gbkfile)

## --------------------------------------------------------------------------
parseGenBank(smpfile, ret.anno=FALSE)

## --------------------------------------------------------------------------
gbr = readGenBank(smpfile)
tx = makeTxDbFromGenBank(gbr)
tx

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genbankr documentation built on Nov. 1, 2018, 3:56 a.m.