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useDynLib(ShortRead, .registration=TRUE)
import(methods)
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData,
ScalarCharacter, ScalarInteger, ScalarLogical,
ScalarNumeric, Versioned, Versions)
importClassesFrom(BiocGenerics, connection)
importClassesFrom(Biostrings, BStringSet, DNAString, DNAStringSet,
PairwiseAlignments, PhredQuality,
QualityScaledDNAStringSet, SolexaQuality,
XStringQuality, XStringSet)
importClassesFrom(GenomicRanges, GRanges, Seqinfo)
importClassesFrom(IRanges, characterORNULL, DataFrame, DataTableORNULL,
FilterRules, IRanges, RangedData, RangesList, Rle,
SimpleList)
importClassesFrom(Rsamtools, BamFileList, RsamtoolsFileList)
importClassesFrom(GenomicAlignments, GAlignments)
importMethodsFrom(IRanges, Ops, coerce)
importMethodsFrom(IRanges, append, as.factor, as.list, as.vector, by,
coerce, colnames, "colnames<-", coverage, diff,
endoapply, eval, gsub, head, ifelse, "%in%", levels,
median, metadata, "metadata<-", narrow, ncol, nrow,
order, paste, pmin, quantile, Reduce, rev, Rle, rownames,
"rownames<-", runLength, runValue, score, sort, split,
start, sub, t, table, tapply, toupper, unique, unlist,
update, Views, which, width, with)
importMethodsFrom(Biobase, "dimLabels<-", initialize, pData, phenoData,
sampleNames, show, varLabels, varMetadata)
importMethodsFrom(BiocGenerics, cbind, density, Filter, get, lapply,
Map, mapply, rbind, sapply, strand)
importMethodsFrom(Biostrings, alphabet, alphabetFrequency, detail,
duplicated, end, match, nchar, pairwiseAlignment,
pattern, PDict, quality, reverse, reverseComplement,
substr, summary, tail, trimLRPatterns, unaligned,
union, vcountPDict)
importMethodsFrom(GenomicRanges, as.data.frame, countOverlaps,
ranges, reduce, seqlevels, "seqlevels<-", seqnames,
values, "values<-")
importMethodsFrom(Rsamtools, isOpen, path, scanBam, ScanBamParam)
importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam,
cigar, left, qnarrow, qwidth, right)
importFrom(Biobase, copySubstitute, mkScalar, selectSome,
subListExtract)
importFrom(BiocParallel, bplapply)
importFrom(Biostrings, BString, BStringSet, DNAString, DNAStringSet,
encoding, get_seqtype_conversion_lookup, mkAllStrings,
QualityScaledDNAStringSet, readDNAStringSet,
writeXStringSet)
importFrom(GenomicRanges, GRanges)
importFrom(grDevices, colorRampPalette, dev.off, jpeg, pdf, png)
importFrom(hwriter, hwrite, hwriteImage)
importFrom(IRanges, DataFrame, FilterRules, IntegerList,
IRanges, isSingleString, isTRUEorFALSE, RleList,
SimpleList, solveUserSEW, subsetByFilter)
importFrom(lattice, dotplot, histogram, levelplot, llines, lsegments,
ltext, panel.abline, panel.dotplot, panel.grid,
panel.histogram, panel.levelplot, panel.xyplot,
strip.custom, xyplot)
importFrom(latticeExtra, xyplot.list)
importFrom(Rsamtools, BamFileList, bamFlagTest, bamReverseComplement,
"bamReverseComplement<-", bamSimpleCigar,
"bamSimpleCigar<-", bamWhat, "bamWhat<-")
importFrom(stats, approxfun, setNames)
importFrom(utils, capture.output, packageDescription, read.csv,
read.table, Sweave)
importFrom(Biostrings, DNA_ALPHABET)
importFrom(GenomicAlignments, GAlignments, cigarToQWidth)
exportClassPattern("^.*$")
exportMethods(show, coerce, dim, length, "[", "[[", alphabetFrequency,
alphabet, coverage, encoding, narrow, strand,
trimLRPatterns, width, append, rbind, "%in%", c, lapply,
sapply)
export(pData, phenoData, varLabels, varMetadata)
exportPattern("^[^\\.]")
S3method(close, ShortReadFile)
S3method(open, ShortReadFile)
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