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##
## Importing
##
import(methods)
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import(S4Vectors)
import(IRanges)
import(GenomicRanges)
import(SummarizedExperiment)
import(DelayedArray)
import(HDF5Array)
import(BiocParallel)
import(limma)
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importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
"combine", "density", "intersect", "lapply", "ncol",
"nrow", "order", "paste", "pmax", "pmin", "rbind",
"Reduce", "rep.int", "rownames", "sapply", "setdiff",
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"strand", "strand<-", "union", "unique", "updateObject", "unstrand")
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importFrom(stats, "approxfun", "fisher.test", "ppoints",
"predict", "preplot", "qchisq",
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"qqplot", "qunif", "cov2cor",
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"setNames")
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importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
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"mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
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import(parallel)
importFrom(locfit, "locfit", "lp")
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importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
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"rowSums2", "rowMeans2", "rowAlls")
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importFrom(scales, "alpha")
importClassesFrom(Biobase, "AnnotatedDataFrame")
importMethodsFrom(Biobase, "annotatedDataFrameFrom",
"pData", "pData<-",
"sampleNames", "sampleNames<-")
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importFrom(Biobase, "validMsg")
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importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
"seqinfo<-", "seqnames", "seqnames<-", "seqlevels",
"seqlevels<-", "sortSeqlevels")
importFrom(GenomeInfoDb, "Seqinfo")
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importFrom(gtools, "combinations")
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importFrom(Rcpp, sourceCpp)
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# NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
# e.g., shift(). If new ones are discovered, add them to this list.
import(data.table, except = c(shift, first, second))
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importFrom(permute, "shuffleSet", "how")
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importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
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importFrom(utils, "read.delim")
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importFrom(BSgenome, "vmatchPattern")
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importFrom(tools, "file_path_as_absolute")
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importFrom(R.utils, "isGzipped", "isBzipped", "gunzip", "bunzip2")
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##
## Exporting
##
exportClasses("hasGRanges",
"BSseq",
"BSseqTstat",
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"BSseqStat",
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"matrixOrNULL")
exportMethods("[", "show",
"seqnames", "seqnames<-",
"seqlevels", "seqlevels<-",
"seqlengths", "seqlengths<-",
"start", "start<-",
"end", "end<-",
"width", "width<-",
"strand", "strand<-",
"granges",
"dim", "nrow", "ncol",
"sampleNames", "sampleNames<-",
"pData", "pData<-",
"findOverlaps", "subsetByOverlaps",
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"combine", "updateObject")
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export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
"collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
"BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
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"combineList", "strandCollapse",
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"plotRegion", "plotManyRegions",
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"read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
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"poissonGoodnessOfFit", "binomialGoodnessOfFit",
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"data.frame2GRanges", "BSseqTstat",
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"BSseqStat",
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"findLoci")
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S3method("print", "chisqGoodnessOfFit")
S3method("plot", "chisqGoodnessOfFit")
S3method("print", "summary.BSseqTstat")
S3method("summary", "BSseqTstat")
S3method("plot", "BSseqTstat")
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## Fixes, to be removed
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exportMethods("assays", "assayNames")
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# C++ code registration
useDynLib(bsseq, .registration = TRUE, .fixes = "cxx_")
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