Included datasets (rda) from the "chromosomes" package to avoid this dependency

Author: aoumess

DESCRIPTION

@@ -7,7 +7,7 @@ Date: 2018-10-30
 Author: Bastien Job
 Maintainer: Bastien JOB <[email protected]>
 Depends: R(>= 3.1.0)
-Imports: affxparser, ASCAT, Biostrings, aroma.light, BSgenome, changepoint, chromosomes, copynumber, data.table, doParallel, dplyr, DT, facets, foreach, GenomeInfoDb, GenomicRanges, iotools, IRanges, limma, mclust, parallel, rhdf5, R.utils, seqinr, sequenza
+Imports: affxparser, ASCAT, Biostrings, aroma.light, BSgenome, changepoint, copynumber, data.table, doParallel, dplyr, DT, facets, foreach, GenomeInfoDb, GenomicRanges, iotools, IRanges, limma, mclust, parallel, rhdf5, R.utils, seqinr, sequenza
 Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, Rsamtools, affy.CN.norm.data, apt.cytoscan.2.4.0, apt.oncoscan.2.4.0, apt.snp6.1.20.0, knitr, rcnorm, rmarkdown
 Description: Easy copy-number analysis for Affymetrix microarrays (snp6.0, CytoScanHD, CytoScan750K & OncoScan) and whole exome sequencing data.
 License: MIT + file LICENSE

NAMESPACE

@@ -1,4 +1,3 @@
-import(chromosomes)
 import(mclust)
 importFrom("affxparser", "readCel", "readCelHeader")
 importFrom("aroma.light", "normalizeTumorBoost")
@@ -11,7 +10,6 @@ importFrom("data.table", "fread")
 importFrom("doParallel", "registerDoParallel")
 importFrom("dplyr", "as.tbl", "group_by", "summarize", "left_join")
 importFrom("DT", "datatable", "formatCurrency", "formatStyle", "formatRound", "styleEqual")
-# importFrom("facets", "emcncf", "scanSnp", "segsnps")
 importFrom("foreach", "foreach", "%do%", "%dopar%")
 importFrom("GenomeInfoDb", "seqlengths")
 importFrom("GenomicRanges", "GRanges", "reduce", "sort", "duplicated", "width", "makeGRangesFromDataFrame", "findOverlaps", "trim")
@@ -25,7 +23,6 @@ importFrom("parallel", "makeCluster", "stopCluster", "detectCores")
 importFrom("R.utils", "gunzip", "bunzip2")
 importFrom("rhdf5", "h5read")
 importFrom("seqinr", "GC")
-# importFrom("sequenza", "baf.bayes", "baf.model.fit", "get.ci")
 importFrom("stats", "approxfun", "density", "end", "mad", "median", "quantile", "runmed", "setNames", "start")
 importFrom("tools", "file_path_as_absolute", "file_ext")
 importFrom("utils", "data", "read.table", "write.table", "count.fields", "installed.packages", "unzip", "head", "tail")

R/EaCoN_functions.R

@@ -2034,7 +2034,7 @@ Annotate <- function(data = NULL, refGene.table = NULL, targets.table = NULL, re
     if (genome %in% names(valid.genomes)) {
       self.pkg.name <- "EaCoN"
       data(list = paste0("refGene_cl_", genome), package = self.pkg.name, envir = environment())
-      data(list = genome, package = "chromosomes", envir = environment())
+      data(list = genome, package = self.pkg.name, envir = environment())
     } else {
       ## ... and none in bank : no genes !
       tmsg("WARNING : No refGene table provided, and none banked for current genome : Gene information won't exist in the report!")
@@ -2601,7 +2601,8 @@ Annotate.solo <- function(cbs.file = NULL, genome = NULL, ldb = "/mnt/data_cigog
   # if (length(cbs.cut.file) > 1) stop(paste0("Found multiple Cut CBS files for ", sample.dir))
   if (!file.exists(cbs.file)) stop(tmsg(paste0("Could not find CBS file [", cbs.file, "] !")))
   cbs.df <- read.table.fast(cbs.file)
-  data(list = genome, package = "chromosomes", envir = environment())
+  self.pkg.name <- "EaCoN"
+  data(list = genome, package = self.pkg.name, envir = environment())
   ## Converting CBS to SOLO
   message(tmsg(" Converting to SOLO ..."))
   solo.df <- data.frame(Loc = paste0(unlist(cs$chr2chrom[cbs.df$Chr]), ":", cbs.df$Start, "-", cbs.df$End), Probes = cbs.df$Probes, Status = sign(cbs.df$Log2Ratio), L2R = cbs.df$Log2Ratio, Ratio = 2^cbs.df$Log2Ratio, stringsAsFactors = FALSE)

R/plot_functions.R

@@ -97,7 +97,8 @@ EaCoN.l2rplot.karyo <- function(l2r = NULL, seg = NULL, seg.col = list(gain = "b
   genome <- BSgenome::providerVersion(BSg.obj)
   # cs <- chromobjector(BSg.obj)
 
-  data(list = genome, package = "chromosomes", envir = environment())
+  self.pkg.name <- "EaCoN"
+  data(list = genome, package = self.pkg.name, envir = environment())
   l2r <- l2r[!is.na(l2r$Value),]
 
   par(mgp=c(0,0,0), omi=c(0,0.2,0.1,0), xaxt="n", yaxt="n", bty="n")
@@ -155,7 +156,8 @@ EaCoN.l2rplot.chromo <- function(chr = NULL, l2r = NULL, l2r.seg = NULL, baf = N
   genome <- BSgenome::providerVersion(BSg.obj)
   # cs <- chromobjector(BSg.obj)
 
-  data(list = genome, package = "chromosomes", envir = environment())
+  self.pkg.name <- "EaCoN"
+  data(list = genome, package = self.pkg.name, envir = environment())
 
   l2r <- l2r[!is.na(l2r$Value),]
   kLprob.idx <- which(l2r$Chr == chr)

README.md

@@ -23,6 +23,7 @@ It consists in a series of R packages that perform such type of analysis, from r
 - Small code changes to adapt to "non-completely covered" genomes (ie, few chromosomes for toy datasets, by example).
 - Harmonized the penalty parameter for all segmenters (now just "penalty" rather than "ASCAT.pen", "SEQUENZA.pen" or "FACETS.pen")
 - Officially dropping support for sequenza with SNP6 arrays as it leads to a huge RAM consumption by copynumber::aspcf, due to the few probes covering both L2R and BAF.
+- Included chromosomes objects in package for hs, mm and rn, to avaoid dependency to another non-public sourceable package.
 
 ### **2018-10-02 : v0.3.3-1 _(LittleWomanNoCry)_ is out !**
 
@@ -124,7 +125,6 @@ While the current EaCoN package is the core of the process, multiple others are
       - GC% & wave-effect normalization :
         - [affy.CN.norm.data](http://bit.ly/AffyCNnorm) _Pre-computed tracks for all supported Affmetrix designs (both hg19 and hg38)_
         - [rcnorm](http://bit.ly/rcnorm) _Code and tracks to re-normalize BAF for the CytoScan family of designs and SNP6, using *rawcopy*_
-        - [chromosomes](http://bit.ly/chromosomespackage) _to provide the structure of chromsomes for homo sapiens (hg17 to hg38, hs37d5), mus musculus (mm7 to mm10) and rattus norvegicus (rn5 to rn6)_
 - Raw data :
   - For Affymetrix microarrays : the **CEL** files, fresh out of the Affymetrix Scanner
   - For WES data :

data/GRCh37-lite.rda

@@ -1,3 +1,15 @@
 refGene_cl_hg19: gen.df
 targetlist_270: targetlist
 targetlist_475: targetlist
+hg17: homo_sapiens_build_17
+hg18: homo_sapiens_build_18
+hg19: homo_sapiens_build_19
+GRCh37-lite: homo_sapiens_build_19_TCGA
+hs37d5: homo_sapiens_build_19_1000Genomes
+hg38: homo_sapiens_build_38
+mm7: mus_musculus_build_7
+mm8: mus_musculus_build_8
+mm9: mus_musculus_build_9
+mm10: mus_musculus_build_10
+rn5: rattus_norvegicus_build_5
+rn6: rattus_norvegicus_build_6