### R code from vignette source 'appreci8R.Rnw' ################################################### ### code chunk number 1: appreci8R.Rnw:21-22 ################################################### options(width=100) ################################################### ### code chunk number 2: 2installing (eval = FALSE) ################################################### ## BiocManager::install("appreci8R") ################################################### ### code chunk number 3: 3loading ################################################### library(appreci8R) ################################################### ### code chunk number 4: 4 ################################################### output_folder<-"" target<-data.frame(chr = c("2","4","12","17","21","X"), start = c(25469500,106196950,12046280,7579470,36164400,15838363), end = c(25469510,106196960,12046350,7579475,36164410,15838366)) target caller_folder <- system.file("extdata", package = "appreci8R") #Input data Sample1: read.table(paste(caller_folder, "/Sample1.rawMutations.vcf", sep=""), header = FALSE, sep = "\t", stringsAsFactors = FALSE) #Input data Sample2: read.table(paste(caller_folder,"/Sample2.rawMutations.vcf",sep=""), header = FALSE, sep = "\t", stringsAsFactors = FALSE) filterTarget(output_folder, "GATK", caller_folder, ".rawMutations", ".vcf", TRUE, "", "", targetRegions = target) ################################################### ### code chunk number 5: 5 ################################################### output_folder <- "" caller_name <- "" sample1 <- data.frame(SampleID = c("Sample1","Sample1","Sample1"), Chr = c("2","17","X"), Pos = c(25469502,7579472,15838366), Ref = c("CAG","G","C"), Alt = c("TAT","C","T,A"), stringsAsFactors = FALSE) sample2 <- data.frame(SampleID = c("Sample2","Sample2","Sample2","sample2"), Chr = c("4","12","12","21"), Pos = c(106196951,12046289,12046341,36164405), Ref = c("A","C","A","GGG"), Alt = c("G","+AAAG","G","TGG"), stringsAsFactors = FALSE) #Input: input <- list(sample1, sample2) input normalized <- appreci8R::normalize(output_folder, caller_name, input, TRUE, TRUE) normalized ################################################### ### code chunk number 6: 6 ################################################### library(GenomicRanges) output_folder <- "" caller_name <- "" input <- GRanges(seqnames = c("2","X","4","21"), ranges = IRanges(start = c (25469504,15838366,106196951,36164405), end = c (25469504,15838366,106196951,36164405)), SampleID = c("Sample1","Sample1","Sample2","Sample2"), Ref = c("G","C","A","G"), Alt = c("T","A","G","T")) #Input: input library(GO.db) library(org.Hs.eg.db) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(Biostrings) annotated <- annotate(output_folder, caller_name, input, locations = c("coding","spliceSite"), consequences = c("nonsynonymous","frameshift","nonsense")) annotated ################################################### ### code chunk number 7: 7 ################################################### output_folder <- "" caller_name <- "" #Input: gatk <- annotated[c(1,3),] varscan <- annotated[c(2,3),] annotated<-GRangesList() annotated[[1]]<-gatk annotated[[2]]<-varscan annotated combined<-combineOutput("", c("GATK","VarScan"), annotated) combined ################################################### ### code chunk number 8: 8 ################################################### output_folder <- "" bam_folder <- system.file("extdata", package = "appreci8R") bam_folder <- paste(bam_folder, "/", sep="") #Input: combined filtered<-evaluateCovAndBQ(output_folder, combined, bam_folder, bq_diff = 20, vaf = 0.001) filtered ################################################### ### code chunk number 9: 9 ################################################### output_folder <- "" #Input: filtered characteristics <- determineCharacteristics(output_folder, filtered, predict = "Provean") characteristics ################################################### ### code chunk number 10: 10 ################################################### output_folder <- "" #Input: filtered characteristics combined final<-finalFiltration(output_folder, frequency_calls = filtered, database_calls = characteristics, combined_calls = combined, damaging_safe = -3, tolerated_safe = -1.5, overlapTools = c("VarScan"), bq_diff = 20,vaf = 0.001) final ################################################### ### code chunk number 11: 11 (eval = FALSE) ################################################### ## appreci8Rshiny()