@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 0.11.5

+Version: 0.99.0

 Title: Analyze, manage and store bisulfite sequencing data

 Description: Tools for analyzing and visualizing bisulfite sequencing data

 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),

@@ -10,7 +10,7 @@ Imports: scales, stats, graphics, Biobase, locfit

 Suggests: RUnit, bsseqData

 Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R 

         utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R

-        gof_stats.R plotting.R fisher.R fixes.R

+        gof_stats.R plotting.R fisher.R

 License: Artistic-2.0

 LazyData: yes

 biocViews: DNAMethylation

@@ -3,7 +3,7 @@ setClass("BSseq", contains = "SummarizedExperiment",

                         parameters = "list"))

 setValidity("BSseq", function(object) {

-    msg <- validMsg(NULL, bsseq:::.checkAssayNames(object, c("Cov", "M")))

+    msg <- validMsg(NULL, .checkAssayNames(object, c("Cov", "M")))

     if(class(rowData(object)) != "GRanges")

         msg <- validMsg(msg, sprintf("object of class '%s' needs to have a 'GRanges' in slot 'rowData'", class(object)))

     ## benchmarking shows that min(assay()) < 0 is faster than any(assay() < 0) if it is false

@@ -12,8 +12,8 @@ dmrFinder <- function(BSseqTstat, cutoff = NULL, qcutoff = c(0.025, 0.975),

     direction[is.na(direction)] <- 0L

     chrs <- as.character(seqnames(BSseqTstat@gr))

     positions <- start(BSseqTstat)

-    regions <- bsseq:::regionFinder3(direction, chr = chrs, pos = positions,

-                                     maxGap = maxGap, verbose = subverbose)

+    regions <- regionFinder3(direction, chr = chrs, positions = positions,

+                             maxGap = maxGap, verbose = subverbose)

     if(is.null(regions$down) && is.null(regions$up))

         return(NULL)

     if(verbose) cat("[dmrFinder] creating dmr data.frame\n")

deleted file mode 100644

@@ -1,78 +0,0 @@

-## findOverlaps_mclapply <- function (query, subject, maxgap = 0L, minoverlap = 1L, 

-##                                    type = c("any", "start", "end", "within", "equal"),

-##                                    select = c("all", "first"), ignore.strand = FALSE,

-##                                    mc.cores = 1, mc.preschedule = TRUE, verbose = FALSE, ...) {

-##     if(!is(query, "GenomicRanges") || !is(subject, "GenomicRanges"))

-##         stop("findOverlaps_mclapply needs 'query' and 'subject' to be 'GenomicRanges'")

-##     if (!isSingleNumber(maxgap) || maxgap < 0) 

-##         stop("'maxgap' must be a non-negative integer")

-##     type <- match.arg(type)

-##     select <- match.arg(select)

-##     seqinfo <- merge(seqinfo(query), seqinfo(subject))

-##     DIM <- c(length(query), length(subject))

-##     if (min(DIM) == 0L) {

-##         matchMatrix <- matrix(integer(0), nrow = 0L, ncol = 2L, 

-##                               dimnames = list(NULL, c("queryHits", "subjectHits")))

-##     }

-##     else {

-##         querySeqnames <- seqnames(query)

-##         querySplitRanges <- splitRanges(querySeqnames)

-##         uniqueQuerySeqnames <- names(querySplitRanges)[sapply(querySplitRanges, length) > 0] # FIX: only keep seqnames with ranges

-##         subjectSeqnames <- seqnames(subject)

-##         subjectSplitRanges <- splitRanges(subjectSeqnames)

-##         uniqueSubjectSeqnames <- names(subjectSplitRanges)[sapply(subjectSplitRanges, length) > 0] # FIX: only keep seqnames with ranges

-##         commonSeqnames <- intersect(uniqueQuerySeqnames, 

-##                                     uniqueSubjectSeqnames)

-##         if (ignore.strand) {

-##             queryStrand <- rep.int(1L, length(query))

-##             subjectStrand <- rep.int(1L, length(subject))

-##         }

-##         else {

-##             queryStrand <- strand(query)

-##             levels(queryStrand) <- c("1", "-1", "0")

-##             queryStrand@values <- as.integer(as.character(runValue(queryStrand)))

-##             queryStrand <- as.vector(queryStrand)

-##             subjectStrand <- strand(subject)

-##             levels(subjectStrand) <- c("1", "-1", "0")

-##             subjectStrand@values <- as.integer(as.character(runValue(subjectStrand)))

-##             subjectStrand <- as.vector(subjectStrand)

-##         }

-##         queryRanges <- unname(ranges(query))

-##         subjectRanges <- unname(ranges(subject))

-##         matchMatrix <- do.call(rbind, mclapply(commonSeqnames, 

-##                                                function(seqnm) {

-##                                                    if(verbose) cat(seqnm, "\n") # FIX : added verbosity

-##                                                    if (isCircular(seqinfo)[seqnm] %in% TRUE) 

-##                                                        circle.length <- seqlengths(seqinfo)[seqnm]

-##                                                    else circle.length <- NA

-##                                                    qIdxs <- querySplitRanges[[seqnm]]

-##                                                    sIdxs <- subjectSplitRanges[[seqnm]]

-##                                                    ## FIX: added ::: tpo get .findOverlaps.circle

-##                                                    overlaps <- GenomicRanges:::.findOverlaps.circle(circle.length, 

-##                                                                                                     seqselect(queryRanges, qIdxs), seqselect(subjectRanges, 

-##                                                                                                                                              sIdxs), maxgap, minoverlap, type)

-##                                                    qHits <- queryHits(overlaps)

-##                                                    sHits <- subjectHits(overlaps)

-##                                                    matches <- cbind(queryHits = as.integer(qIdxs)[qHits], 

-##                                                                     subjectHits = as.integer(sIdxs)[sHits])

-##                                                    matches[which(seqselect(queryStrand, qIdxs)[qHits] * 

-##                                                                  seqselect(subjectStrand, sIdxs)[sHits] != 

-##                                                                  -1L), , drop = FALSE]

-##                                                }, mc.cores = mc.cores, mc.preschedule = mc.preschedule))

-##         if (is.null(matchMatrix)) {

-##                 matchMatrix <- matrix(integer(0), nrow = 0L, 

-##                                       ncol = 2L, dimnames = list(NULL, c("queryHits", 

-##                                                  "subjectHits")))

-##             }

-##         matchMatrix <- matchMatrix[IRanges:::orderIntegerPairs(matchMatrix[, 

-##                                                                            1L], matchMatrix[, 2L]), , drop = FALSE]

-##     }

-##     if (select == "all") {

-##         new("Hits", queryHits = unname(matchMatrix[, 1L]), 

-##             subjectHits = unname(matchMatrix[, 2L]), queryLength = DIM[1], 

-##             subjectLength = DIM[2])

-##     }

-##     else {

-##         IRanges:::.hitsMatrixToVector(matchMatrix, length(query))

-##     }

-## }

@@ -176,7 +176,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

     coverage <- getCoverage(BSseq)

     ## get col, lwd, lty

-    colEtc <- bsseq:::.bsGetCol(object = BSseq, col = col, lty = lty, lwd = lwd)

+    colEtc <- .bsGetCol(object = BSseq, col = col, lty = lty, lwd = lwd)

     ## The actual plotting

     plot(positions[1], 0.5, type = "n", xaxt = "n", yaxt = "n",

@@ -224,10 +224,10 @@ plotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions =

     else

         layout(matrix(1:3, ncol = 1), heights = c(2,2,1))

-    bsseq:::.plotSmoothData(BSseq = BSseq, region = region, extend = extend, addRegions = addRegions,

-                            col = col, lty = lty, lwd = lwd, regionCol = regionCol,

-                            addTicks = addTicks, addPoints = addPoints,

-                            pointsMinCov = pointsMinCov, highlightMain = highlightMain)

+    .plotSmoothData(BSseq = BSseq, region = region, extend = extend, addRegions = addRegions,

+                    col = col, lty = lty, lwd = lwd, regionCol = regionCol,

+                    addTicks = addTicks, addPoints = addPoints,

+                    pointsMinCov = pointsMinCov, highlightMain = highlightMain)

     gr <- .bsGetGr(BSseq, region, extend)

     if(!is.null(BSseqTstat)) {

@@ -237,17 +237,17 @@ plotRegion <- function(BSseq, region = NULL, extend = 0, main = "", addRegions =

         axis(side = 2, at = c(-5,0,5))

         abline(h = 0, col = "grey60")

         mapply(function(stat, col, lty, lwd) {

-            bsseq:::.bsPlotLines(start(BSseqTstat), BSseqTstat@stats[, stat],

-                                 lty = lty, plotRange = c(start(gr), end(gr)), col = col, lwd = lwd)

+            .bsPlotLines(start(BSseqTstat), BSseqTstat@stats[, stat],

+                         lty = lty, plotRange = c(start(gr), end(gr)), col = col, lwd = lwd)

         }, stat = stat, col = stat.col, lty = stat.lty, lwd = stat.lwd)

     }

     if(!is.null(annoTrack))

-        bsseq:::plotAnnoTrack(gr, annoTrack)

+        plotAnnoTrack(gr, annoTrack)

     if(!is.null(main)) {

-        main <- bsseq:::.bsPlotTitle(gr = region, extend = extend, main = main,

-                                     mainWithWidth = mainWithWidth)

+        main <- .bsPlotTitle(gr = region, extend = extend, main = main,

+                             mainWithWidth = mainWithWidth)

         mtext(side = 3, text = main, outer = TRUE, cex = 1)

     }

     return(invisible(NULL))

@@ -472,9 +472,9 @@ parsingPipeline <- function(dirs, qualityCutoff = 20, outDir, seqnames = NULL,

         base <- basename(dir)

         cat("parsing, ")

         ptime1 <- proc.time()

-        raw <- bsseq:::read.bsmoothDirRaw(file.path(dir, subdir),

-                                          keepCycle = TRUE, keepFilt = TRUE,

-                                          verbose = FALSE)

+        raw <- read.bsmoothDirRaw(file.path(dir, subdir),

+                                  keepCycle = TRUE, keepFilt = TRUE,

+                                  verbose = FALSE)

         assign(paste0(base, ".raw"), raw)

         ptime2 <- proc.time()

         stime <- (ptime2 - ptime1)[3]

@@ -487,8 +487,8 @@ parsingPipeline <- function(dirs, qualityCutoff = 20, outDir, seqnames = NULL,

              file = file.path(outDir, paste0(base, ".raw.rda")))

         cat("converting, ")

         ptime1 <- proc.time()

-        bsseq <- bsseq:::sampleRawToBSseq(raw, qualityCutoff = qualityCutoff,

-                                          sampleName = base)

+        bsseq <- sampleRawToBSseq(raw, qualityCutoff = qualityCutoff,

+                                  sampleName = base)

         seqlevels(bsseq)[seqlevels(bsseq) == "chrgi|9626243|ref|NC_001416.1|"] <- "chrLambda"

         ptime2 <- proc.time()

         stime <- (ptime2 - ptime1)[3]

@@ -20,8 +20,8 @@ test_BSseq <- function() {

     checkEquals(dim(BStest), c(3,3))

     checkEquals(nrow(BStest), 3)

     checkEquals(ncol(BStest), 3)

-    checkEquals(getCoverage(BStest, type = "M"), unname(M))

-    checkEquals(getCoverage(BStest, type = "Cov"), unname(M + 2))

+    checkEquals(unname(getCoverage(BStest, type = "M")), unname(M))

+    checkEquals(unname(getCoverage(BStest, type = "Cov")), unname(M + 2))

     checkEquals(sampleNames(BStest), colnames(M))

     BStest2 <- BSseq(pos = 3:1, chr = rep("chr1", 3), M = M[3:1,],