## ----eval=FALSE---------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("nanotatoR", version = "3.8") ## ----eval=TRUE----------------------------------------------------------- library("nanotatoR") ## ----eval=TRUE----------------------------------------------------------- decipherpath <- system.file("extdata", "population_cnv.txt", package = "nanotatoR") smapName <- "F1.1_TestSample1_solo_hg19.smap" smappath <- system.file("extdata", package = "nanotatoR") win_indel=10000;win_inv_trans=50000;perc_similarity=0.5 decipherext<-Decipher_extraction(decipherpath, input_fmt = "Text", smappath, smap= smapName, win_indel = 10000, perc_similarity = 0.5, returnMethod="dataFrame") ## ----eval=TRUE----------------------------------------------------------- mergedFiles <- system.file("extdata", "BNSOLO2_merged.txt", package = "nanotatoR") smapName <- "F1.1_TestSample1_solo_hg19.smap" smappath <- system.file("extdata", package = "nanotatoR") win_indel = 10000; win_inv_trans = 50000; perc_similarity = 0.5; indelconf = 0.5; invconf = 0.01;transconf = 0.1 cohortFreq<-cohortFrequency(internalBNDB = mergedFiles , smappath , smap=smapName, input_fmt ="Text", buildBNInternalDB=FALSE, win_indel, win_inv_trans, perc_similarity , indelconf, invconf, transconf,returnMethod="dataFrame") ## ----eval=TRUE----------------------------------------------------------- mergedFiles <- system.file("extdata", "nanotatoR_merged.txt", package = "nanotatoR") smapName <- "F1.1_TestSample1_solo_hg19.smap" smappath <- system.file("extdata", package = "nanotatoR") intFreq <- internalFrequency(mergedFiles = mergedFiles, smappath = smappath , smap = smapName, buildSVInternalDB=FALSE, win_indel=10000, win_inv_trans=50000, perc_similarity=0.5, indelconf=0.5, invconf=0.01, transconf=0.1, limsize=1000, win_indel_parents=5000,input_fmt="Text", win_inv_trans_parents=40000, returnMethod="dataFrame") intFreq [1,] ## ----eval=TRUE----------------------------------------------------------- smapName="F1.1_TestSample1_solo_hg19.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "Homo_sapiens.Hg19_BN_bed.txt", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp <- compSmapbed(smap, bed=bedFile, inputfmtBed = "BNBED", n = 3, returnMethod_bedcomp = c("dataFrame")) datcomp[1,] ## ----eval=TRUE----------------------------------------------------------- terms="Muscle Weakness" gene <- gene_list_generation(method="Single", term=terms, returnMethod="dataFrame") gene[1:10,] ## ----eval=FALSE---------------------------------------------------------- # terms <- "Muscle Weakness" # gene <- gene_list_generation( # method = "Single", term = terms, # returnMethod_GeneList = "dataFrame" # ) # RzipFile = "zip.exe" # RZIPpath <- system.file("extdata", RzipFile, package = "nanotatoR") # smapName <- "F1.1_TestSample1_solo_hg19.smap" # smappath <- system.file("extdata", smapName, package = "nanotatoR") # smappath1 <- system.file("extdata", package = "nanotatoR") # run_bionano_filter(input_fmt_geneList = c("dataframe"), # input_fmt_svMap = c("Text"), # SVFile = smappath, dat_geneList = gene, # outpath = smappath1, outputFilename = "test", # RZIPpath = RZIPpath) ## ----eval=FALSE---------------------------------------------------------- # terms <- "Muscle Weakness" # gene <- gene_list_generation( # method = "Single", term = terms, # returnMethod = "dataFrame" # ) # mergedFiles <- system.file ("extdata", "BNSOLO2_merged.txt", # package = "nanotatoR") # RzipFile = "zip.exe" # RZIPpath <- system.file("extdata", RzipFile, package = "nanotatoR") # smapName <- "F1.1_TestSample1_solo_hg19.smap" # smappath <- system.file("extdata", smapName, package = "nanotatoR") # path <- system.file("extdata", "SoloFile/", package = "nanotatoR") # hgpath <- system.file ("extdata", "GRCh37_hg19_variants_2016-05-15.txt", package = "nanotatoR") # decipherpath <- system.file("extdata", "population_cnv.txt", package = "nanotatoR") # bedFile <- system.file("extdata", "Homo_sapiens.Hg19.bed", package="nanotatoR") # pattern <- "_hg19.smap" # nanotatoR_main(smap = smappath, bed = bedFile, # inputfmtBed = c("BNBED"), # n = 3, buildSVInternalDB = TRUE, soloPath = path, solopattern = pattern, # input_fmt_INF = c("dataFrame"), buildBNInternalDB = FALSE, # returnMethod_bedcomp = c("dataFrame"), returnMethod_DGV = c("dataFrame"), # returnMethod_Internal = c("dataFrame"), input_fmt_DGV = c("dataFrame"), # hgpath = hgpath, smapName = smapName, limsize=1000, win_indel_parents=5000, # decipherpath = decipherpath, dbOutput_Int = "dataframe", # win_inv_trans_parents=40000, win_indel_DGV = 10000, # input_fmt_geneList = c("dataFrame"), input_fmt_svMap = c("dataFrame"), # input_fmt_decipher = "dataFrame",input_fmt_BN = "dataFrame", # returnMethod_GeneList = c("dataFrame"),returnMethod_BNCohort = c("dataFrame"), # returnMethod_decipher = c("dataFrame"), mergedFiles_BN = mergedFiles, # dat_geneList = gene , method_entrez = "", # outpath = smappath, outputFilename = "test", # RZIPpath = RZIPpath)