signature.tools.lib.develop.R

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

#file with commands to set up the signature-tools-lib R package
#setwd("~/sandbox/git")

# install.packages("devtools")
# install.packages("roxygen2")
#
# devtools::create("signature.tools.lib")

devtools::use_package("VariantAnnotation")
devtools::use_package("SummarizedExperiment")
devtools::use_package("BiocGenerics")
devtools::use_package("GenomeInfoDb")
devtools::use_package("BSgenome")
devtools::use_package("BSgenome.Hsapiens.UCSC.hg38")
devtools::use_package("BSgenome.Hsapiens.1000genomes.hs37d5")
devtools::use_package("BSgenome.Mmusculus.UCSC.mm10")
devtools::use_package("BSgenome.Cfamiliaris.UCSC.canFam3")
devtools::use_package("NMF")
devtools::use_package("foreach")
devtools::use_package("doParallel")
devtools::use_package("lpSolve")
devtools::use_package("methods")
devtools::use_package("cluster")
devtools::use_package("stats")
devtools::use_package("NNLM")
devtools::use_package("nnls")
devtools::use_package("GenSA")
devtools::use_package("gmp")
devtools::use_package("plyr")
devtools::use_package("RCircos")
devtools::use_package("scales")
devtools::use_package("GenomicRanges")
devtools::use_package("IRanges")
devtools::load_all()

#add internal data
RS.Breast560 <- read.table("data/Breast560_rearrangement.signatures.txt", sep="\t", header=T, as.is=T, check.names = FALSE)
cosmic30 <- read.table("data/COSMIC30_subs_signatures.txt", sep="\t", header=T, as.is=T, check.names = FALSE)
all_organ_sigs_subs <- read.table("data/2019_01_10_all_PCAWG_sigs_subs.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
all_organ_sigs_rearr <- read.table("data/2019_01_10_all_PCAWG_sigs_rearr.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
conversion_matrix_subs <- read.table("data/2019_01_10_ConversionMatrix_subs.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
conversion_matrix_rearr <- read.table("data/2019_01_10_ConversionMatrix_rearr.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
RefSigv1_subs <- read.table("data/RefSigv1_Subs.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
RefSigv1_rearr <- read.table("data/RefSigv1_Rearr.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)

load("data/chrominfo.RData")
load("data/chrominfo.snp6.hg19.RData")

organSignaturesSBSv2.03 <- cbind(readTable("data/RefSigSBS_v2.03/OrganSpecificSigs_GEL_SBS_v2.03.tsv"),
                            readTable("data/RefSigSBS_v2.03/OrganSpecificSigs_ICGC_SBS_v2.03.tsv"),
                            readTable("data/RefSigSBS_v2.03/OrganSpecificSigs_Hartwig_SBS_v2.03.tsv"))
conversionMatrixSBSv2.03 <- readTable("data/RefSigSBS_v2.03/RefSig_SBS_conversionMatrix_v2.03.tsv")
referenceSignaturesSBSv2.03 <- readTable("data/RefSigSBS_v2.03/RefSig_SBS_v2.03.tsv")
sigsForFittingSBSv2.03 <- readTable("data/RefSigSBS_v2.03/SigsForFitting_SBS_v2.03.tsv")

organSignaturesDBSv1.01 <- cbind(readTable("data/RefSigDBS_v1.01//OrganSpecificSigs_GEL_DBS_v1.01.tsv"),
                                 readTable("data/RefSigDBS_v1.01/OrganSpecificSigs_ICGC_DBS_v1.01.tsv"),
                                 readTable("data/RefSigDBS_v1.01/OrganSpecificSigs_Hartwig_DBS_v1.01.tsv"))
conversionMatrixDBSv1.01 <- readTable("data/RefSigDBS_v1.01/RefSig_DBS_conversionMatrix_v1.01.tsv")
referenceSignaturesDBSv1.01 <- readTable("data/RefSigDBS_v1.01/RefSig_DBS_v1.01.tsv")
sigsForFittingDBSv1.01 <- readTable("data/RefSigDBS_v1.01/SigsForFitting_DBS_v1.01.tsv")

COSMIC_v3.2_SBS_GRCh37 <- readTable("data/COSMIC_v3.2_SBS_GRCh37.tsv")
rownames(COSMIC_v3.2_SBS_GRCh37) <- COSMIC_v3.2_SBS_GRCh37$Type
COSMIC_v3.2_SBS_GRCh37 <- sortCatalogue(COSMIC_v3.2_SBS_GRCh37[,-1,drop=F])
COSMIC_v3.2_DBS_GRCh37 <- readTable("data/COSMIC_v3.2_DBS_GRCh37.tsv")
rownames(COSMIC_v3.2_DBS_GRCh37) <- COSMIC_v3.2_DBS_GRCh37$Type
COSMIC_v3.2_DBS_GRCh37 <- COSMIC_v3.2_DBS_GRCh37[,-1,drop=F]


strandBiasTable <- read.table("data/StrandBiasTable.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
strandBiasCounts_single <- read.table("data/StrandBiasTable_Counts_Pyr_single.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)
strandBiasCounts_tri <- read.table("data/StrandBiasTable_Counts_Pyr_tri.tsv", sep="\t", header=T, as.is=T, check.names = FALSE)

usethis::use_data(RS.Breast560,
                  cosmic30,
                  chrominfo,
                  chrominfo.snp6,
                  all_organ_sigs_subs,
                  all_organ_sigs_rearr,
                  conversion_matrix_subs,
                  conversion_matrix_rearr,
                  organSignaturesSBSv2.03,
                  conversionMatrixSBSv2.03,
                  referenceSignaturesSBSv2.03,
                  sigsForFittingSBSv2.03,
                  organSignaturesDBSv1.01,
                  conversionMatrixDBSv1.01,
                  referenceSignaturesDBSv1.01,
                  sigsForFittingDBSv1.01,
                  RefSigv1_subs,
                  RefSigv1_rearr,
                  COSMIC_v3.2_SBS_GRCh37,
                  COSMIC_v3.2_DBS_GRCh37,
                  strandBiasTable,
                  strandBiasCounts_single,
                  strandBiasCounts_tri,
                  internal = TRUE,
                  overwrite = TRUE)

devtools::document()
devtools::install()
# devtools::install(dependencies = FALSE)

#test all
devtools::test()

#some individual tests
devtools::test(pkg = ".",filter = "ascatToHRDLOH")
devtools::test(pkg = ".",filter = "tabToIndelsClassification")
devtools::test(pkg = ".",filter = "vcfToIndelsClassification")
devtools::test(pkg = ".",filter = "HRDetect")
devtools::test(pkg = ".",filter = "tabToSNVcatalogue")
devtools::test(pkg = ".",filter = "vcfToSNVcatalogue")
devtools::test(pkg = ".",filter = "bedpeToRearrCatalogue")
devtools::test(pkg = ".",filter = "genomePlot")
devtools::test(pkg = ".",filter = "SignatureExtraction")
devtools::test(pkg = ".",filter = "SignaturePartialExtraction")
devtools::test(pkg = ".",filter = "SignatureFit")
devtools::test(pkg = ".",filter = "snvTabToDNVcatalogue")
devtools::test(pkg = ".",filter = "vcfToDNVcatalogue")
devtools::test(pkg = ".",filter = "tabToDNVcatalogue")
devtools::test(pkg = ".",filter = "DNVTNVfunctions")
devtools::test(pkg = ".",filter = "organSpecificSignatures")
devtools::test(pkg = ".",filter = "plotCopyNumbers")
devtools::test(pkg = ".",filter = "FitAndFitMS")
devtools::test(pkg = ".",filter = "FitAndFitMS_DBS")
devtools::test(pkg = ".",filter = "JSONexport")
devtools::test(pkg = ".",filter = "SignatureFit_pipeline")
devtools::test(pkg = ".",filter = "matchClustering")
devtools::test(pkg = ".",filter = "assignSignatureProbabilityToMutations")
devtools::test(pkg = ".",filter = "strandBias")
devtools::test(pkg = ".",filter = "mutationContext")
devtools::test(pkg = ".",filter = "genomeChart")
devtools::test(pkg = ".",filter = "plotRegion")