## ---- include=FALSE----------------------------------------------------------- library(knitr) opts_chunk$set(concordance=FALSE) knitr::opts_chunk$set(fig.width = 8) knitr::opts_chunk$set(fig.height = 5) set.seed(21666641) ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("CNVfilteR") ## ---- eval = FALSE------------------------------------------------------------ # BiocManager::install("jpuntomarcos/CNVfilteR") ## ----message=FALSE------------------------------------------------------------ library(CNVfilteR) cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE) cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample", genome = "hg19") ## ----------------------------------------------------------------------------- vcf.files <- c(system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE), system.file("extdata", "variants.sample2.vcf.gz", package = "CNVfilteR", mustWork = TRUE)) vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr, genome = "hg19") ## ----message=FALSE------------------------------------------------------------ results <- filterCNVs(cnvs.gr, vcfs) names(results) ## ----------------------------------------------------------------------------- results$cnvs[results$cnvs$filter == TRUE] ## ----------------------------------------------------------------------------- results$variantsForEachCNV[["3"]] ## ---- fig.wide=TRUE----------------------------------------------------------- plotVariantsForCNV(results, "3") ## ---- fig.wide=TRUE----------------------------------------------------------- plotVariantsForCNV(results, "19") ## ----------------------------------------------------------------------------- results$cnvs[results$cnvs$filter != TRUE] ## ----------------------------------------------------------------------------- results$variantsForEachCNV[["14"]] ## ---- fig.wide=TRUE----------------------------------------------------------- plotVariantsForCNV(results, "3") ## ----message=FALSE------------------------------------------------------------ cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE) cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample", genome = "hg19") ## ----eval=FALSE--------------------------------------------------------------- # cnvs.gr.2 <- loadCNVcalls(cnvs.file = cnvs.file.2, deletion = "CN1", duplication = "CN3", chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample") ## ----------------------------------------------------------------------------- vcf.files <- c(system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE), system.file("extdata", "variants.sample2.vcf.gz", package = "CNVfilteR", mustWork = TRUE)) vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr) ## ----------------------------------------------------------------------------- vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr, vcf.source = "MyCaller", ref.support.field = "RD", alt.support.field = "AD") ## ----------------------------------------------------------------------------- vcf.file3 <- c(system.file("extdata", "variants.sample3.vcf", package = "CNVfilteR", mustWork = TRUE)) vcfs3 <- loadVCFs(vcf.file3, cnvs.gr = cnvs.gr, vcf.source = "MyCaller", list.support.field = "AD") ## ----------------------------------------------------------------------------- regions.to.exclude <- GRanges(seqnames = c("chr3","chr7", "chr7"), ranges = IRanges(c(10068098, 6012870, 142457319), c(10143614, 6048756, 142460923))) vcfs4 <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr, regions.to.exclude = regions.to.exclude) ## ----------------------------------------------------------------------------- results <- filterCNVs(cnvs.gr, vcfs) tail(results$cnvs) ## ---- fig.height=6, fig.wide=TRUE--------------------------------------------- p <- results$filterParameters plotScoringModel(expected.ht.mean = p$expected.ht.mean, expected.dup.ht.mean1 = p$expected.dup.ht.mean1, expected.dup.ht.mean2 = p$expected.dup.ht.mean2, sigmoid.c1 = p$sigmoid.c1, sigmoid.c2.vector = p$sigmoid.c2.vector) ## ---- fig.height=6, fig.wide=TRUE--------------------------------------------- plotScoringModel(expected.ht.mean = p$expected.ht.mean, expected.dup.ht.mean1 = p$expected.dup.ht.mean1, expected.dup.ht.mean2 = p$expected.dup.ht.mean2, sigmoid.c1 = 1, sigmoid.c2.vector = p$sigmoid.c2.vector) ## ---- fig.height=6, fig.wide=TRUE--------------------------------------------- plotScoringModel(expected.ht.mean = p$expected.ht.mean, expected.dup.ht.mean1 = p$expected.dup.ht.mean1, expected.dup.ht.mean2 = p$expected.dup.ht.mean2, sigmoid.c1 = p$sigmoid.c1, sigmoid.c2.vector = c(28, 38.3, 46.7, 53.3, 61.3, 71.3)) ## ---- fig.wide=TRUE----------------------------------------------------------- plotVariantsForCNV(results, "16") ## ---- fig.width=8, fig.height=8, fig.wide=TRUE-------------------------------- cnvs.file <- system.file("extdata", "DECoN.CNVcalls.2.csv", package = "CNVfilteR", mustWork = TRUE) cnvs.gr.2 <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample", genome = "hg19") plotAllCNVs(cnvs.gr.2) ## ----------------------------------------------------------------------------- sessionInfo()