@@ -3,7 +3,6 @@

 export(annotateTargets)

 export(bootstrapResults)

 export(calculateBamCoverageByInterval)

-export(calculateGCContentByInterval)

 export(calculateLogRatio)

 export(calculateMappingBiasVcf)

 export(calculatePowerDetectSomatic)

@@ -20,12 +19,10 @@ export(filterTargets)

 export(filterVcfBasic)

 export(filterVcfMuTect)

 export(filterVcfMuTect2)

-export(findBestNormal)

 export(findFocal)

 export(getSexFromCoverage)

 export(getSexFromVcf)

 export(plotAbs)

-export(plotBestNormal)

 export(poolCoverage)

 export(predictSomatic)

 export(preprocessIntervals)

@@ -42,7 +42,7 @@ globalVariables(names=c("..level.."))

 #'             scale_alpha_continuous scale_y_sqrt geom_abline

 #'             coord_trans

 #' @importFrom gridExtra grid.arrange

-#' @importFrom stats loess lm

+#' @importFrom stats loess lm predict

 #' @importFrom utils write.table

 correctCoverageBias <- function(coverage.file, interval.file,

 output.file = NULL, plot.bias = FALSE, plot.max.density = 50000, 

@@ -111,12 +111,13 @@ min.coverage = 0.25, max.missing = 0.03, low.coverage = 15, ...) {

     }

     list(

-        normal.coverage.files = normal.coverage.files, 

+        normal.coverage.files = normal.coverage.files,

+        intervals = as.character(normals[[1]]),

         groups = groups,

         intervals.used = intervals.used,

         sex = sex,

         low.coverage.targets = low.coverage.targets,

-        version = 5

+        version = 6

     )

 }

@@ -100,8 +100,12 @@ filterTargets <- function(normal, tumor, log.ratio, seg.file,

         !length(normalDB$normal.coverage.files)) {

         .stopUserError("normalDB appears to be empty.")

     }    

-    tmp <- readCoverageFile(normalDB$normal.coverage.files[1])

-    return(identical(as.character(tmp), as.character(tumor)))

+    intervals <- normalDB$intervals

+    # TODO remove in PureCN 1.14 

+    if (is.null(intervals)) {

+        intervals <- as.character(readCoverageFile(normalDB$normal.coverage.files[1]))

+    }

+    return(identical(intervals, as.character(tumor)))

 }

 .filterTargetsNotNA <- function(log.ratio) {

@@ -1,51 +1,9 @@

 #' Find best normal sample in database

 #' 

 #' Function to find the best matching normal for a provided tumor sample.

-#' This function is deprecated and most features are not relevant with

-#' the replacement function \code{\link{calculateTangentNormal}}.

+#' This function is defunct and replaced by

+#' \code{\link{calculateTangentNormal}}.

 #' 

-#' 

-#' @param tumor.coverage.file Coverage file or data of a tumor sample.

-#' @param normalDB Database of normal samples, created with

-#' \code{\link{createNormalDatabase}}.

-#' @param pcs Principal components to use for distance calculation.

-#' @param num.normals Return the \code{num.normals} best normals.

-#' @param ignore.sex If \code{FALSE}, detects sex of sample and returns best

-#' normals with matching sex.

-#' @param sex Sex of sample. If \code{NULL}, determine with

-#' \code{\link{getSexFromCoverage}} and default parameters. Valid values are

-#' \code{F} for female, \code{M} for male. If all chromosomes are diploid,

-#' specify \code{diploid}.

-#' @param normal.coverage.files Only consider these normal samples. If

-#' \code{NULL}, use all in the database. Must match

-#' \code{normalDB$normal.coverage.files}.

-#' @param pool If \code{TRUE}, use \code{\link{poolCoverage}} to pool best

-#' normals.

-#' @param pool.weights Either find good pooling weights by optimization or

-#' weight all best normals equally.

-#' @param plot.pool Allows the pooling function to create plots.

-#' @param \dots Additional arguments passed to \code{\link{poolCoverage}}.

-#' @return Filename of the best matching normal.

-#' @author Markus Riester

-#' @seealso \code{\link{createNormalDatabase} \link{getSexFromCoverage}}

-#' @export findBestNormal

-#' @importFrom stats dist predict

-findBestNormal <- function(tumor.coverage.file, normalDB, pcs=1:3, 

-    num.normals = 1, ignore.sex = FALSE, sex = NULL, 

-    normal.coverage.files = NULL, pool = FALSE, 

-    pool.weights = c("voom", "equal"), plot.pool = FALSE, 

-    ...) {

-    .Deprecated("calculateTangentNormal")

-    calculateTangentNormal(tumor.coverage.file, normalDB, ignore.sex = ignore.sex, 

-        sex = sex)

-}

-

-

-#' Plot the PCA of tumor and its best normal(s)

-#' 

-#' This method is defunct with no replacement

-#' 

-#' @export plotBestNormal

-plotBestNormal <- function() {

-    .Defunct()

+findBestNormal <- function() {

+    .Defunct("calculateTangentNormal")

 }

@@ -124,12 +124,8 @@ preprocessIntervals <- function(interval.file, reference.file,

 #'

 #' This function was renamed to \code{\link{preprocessIntervals}}.

 #'

-#' @param ... Arguments passed to \code{\link{preprocessIntervals}}.

-#' 

-#' @export calculateGCContentByInterval

-calculateGCContentByInterval <- function(...) {

-    .Deprecated("preprocessIntervals")

-    preprocessIntervals(...)

+calculateGCContentByInterval <- function() {

+    .Defunct("preprocessIntervals")

 }    

 # this function removes short chromosomes that have no probes (mainly a

@@ -68,7 +68,7 @@

 #'     fun.segmentation=segmentationCBS, args.segmentation=list(alpha=0.001))

 #' 

 #' @export segmentationCBS

-#' @importFrom stats t.test hclust cutree

+#' @importFrom stats t.test hclust cutree dist

 segmentationCBS <- function(normal, tumor, log.ratio, seg, plot.cnv, 

     sampleid, target.weight.file = NULL, alpha = 0.005, undo.SD =

         NULL, vcf = NULL, tumor.id.in.vcf = 1, normal.id.in.vcf = NULL,

@@ -11,8 +11,10 @@

   the replacement indicated below:

   \itemize{

     \item{autoCurateResults: no replacement}

+    \item{calculateGCContentByInterval: \code{\link{preprocessIntervals}}}

     \item{createExonWeightFile: \code{\link{createTargetWeights}}}

     \item{createSNPBlacklist: \code{\link{setMappingBiasVcf}}}

+    \item{findBestNormal: \code{\link{calculateTangentNormal}}}

     \item{getDiploid: no replacement}

     \item{plotBestNormal: no replacement}

     \item{readCoverageGatk: \code{\link{readCoverageFile}}}

@@ -11,7 +11,6 @@

   The following functions are deprecated and will be made defunct; use

   the replacement indicated below:

   \itemize{

-    \item{calculateGCContentByInterval: \code{\link{preprocessIntervals}}}

-    \item{findBestNormal: \code{\link{calculateTangentNormal}}}

+    \item{none}

   }

 }

@@ -4,10 +4,7 @@

 \alias{calculateGCContentByInterval}

 \title{Calculates GC content by interval}

 \usage{

-calculateGCContentByInterval(...)

-}

-\arguments{

-\item{...}{Arguments passed to \code{\link{preprocessIntervals}}.}

+calculateGCContentByInterval()

 }

 \description{

 This function was renamed to \code{\link{preprocessIntervals}}.

@@ -4,53 +4,10 @@

 \alias{findBestNormal}

 \title{Find best normal sample in database}

 \usage{

-findBestNormal(tumor.coverage.file, normalDB, pcs = 1:3, num.normals = 1,

-  ignore.sex = FALSE, sex = NULL, normal.coverage.files = NULL,

-  pool = FALSE, pool.weights = c("voom", "equal"), plot.pool = FALSE, ...)

-}

-\arguments{

-\item{tumor.coverage.file}{Coverage file or data of a tumor sample.}

-

-\item{normalDB}{Database of normal samples, created with

-\code{\link{createNormalDatabase}}.}

-

-\item{pcs}{Principal components to use for distance calculation.}

-

-\item{num.normals}{Return the \code{num.normals} best normals.}

-

-\item{ignore.sex}{If \code{FALSE}, detects sex of sample and returns best

-normals with matching sex.}

-

-\item{sex}{Sex of sample. If \code{NULL}, determine with

-\code{\link{getSexFromCoverage}} and default parameters. Valid values are

-\code{F} for female, \code{M} for male. If all chromosomes are diploid,

-specify \code{diploid}.}

-

-\item{normal.coverage.files}{Only consider these normal samples. If

-\code{NULL}, use all in the database. Must match

-\code{normalDB$normal.coverage.files}.}

-

-\item{pool}{If \code{TRUE}, use \code{\link{poolCoverage}} to pool best

-normals.}

-

-\item{pool.weights}{Either find good pooling weights by optimization or

-weight all best normals equally.}

-

-\item{plot.pool}{Allows the pooling function to create plots.}

-

-\item{\dots}{Additional arguments passed to \code{\link{poolCoverage}}.}

-}

-\value{

-Filename of the best matching normal.

+findBestNormal()

 }

 \description{

 Function to find the best matching normal for a provided tumor sample.

-This function is deprecated and most features are not relevant with

-the replacement function \code{\link{calculateTangentNormal}}.

-}

-\seealso{

-\code{\link{createNormalDatabase} \link{getSexFromCoverage}}

-}

-\author{

-Markus Riester

+This function is defunct and replaced by

+\code{\link{calculateTangentNormal}}.

 }

deleted file mode 100644

@@ -1,11 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/findBestNormal.R

-\name{plotBestNormal}

-\alias{plotBestNormal}

-\title{Plot the PCA of tumor and its best normal(s)}

-\usage{

-plotBestNormal()

-}

-\description{

-This method is defunct with no replacement

-}

@@ -15,6 +15,7 @@ test_that("NormalDB of example data matches expectated values", {

     n <- lapply(normal.coverage.files, readCoverageFile)

     expect_equal(length(pool), length(n[[1]]))

+    expect_equal(as.character(n[[1]]), normalDB$intervals)

  })

 test_that("Provided sex is handled correctly", {

@@ -37,7 +37,7 @@ test_that("skipping base quality works", {

     f1 <- filterVcfBasic(vcf, min.base.quality=NULL)

     f2 <- filterVcfBasic(vcf, min.base.quality=0)

     expect_equal(length(f1$vcf), length(f2$vcf))

-}

+})

 test_that("M2 VCF with POP_AF flag is annotated with DB flag", {

     # first check that the POP_AF field is parsed