## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("nanotatoR", version = "3.8") ## ----eval=TRUE---------------------------------------------------------------- library("nanotatoR") ## ----eval=TRUE---------------------------------------------------------------- hgpath=system.file("extdata", "GRCh37_hg19_variants_2016-05-15.txt", package="nanotatoR") smappath=system.file("extdata", "GM24385_Ason_DLE1_VAP_trio5.smap", package="nanotatoR") datDGV <- DGVfrequency (hgpath = hgpath, smap = smappath, EnzymeType = "SE", win_indel_DGV = 10000, win_inv_trans_DGV = 50000, input_fmt_SV = "Text", perc_similarity_DGV = 0.5,returnMethod="dataFrame") datDGV[1,] ## ----eval=TRUE---------------------------------------------------------------- decipherpath = system.file("extdata", "population_cnv.txt", package="nanotatoR") smappath=system.file("extdata", "GM24385_Ason_DLE1_VAP_trio5.smap", package="nanotatoR") datdecipher <- Decipherfrequency (decipherpath = decipherpath, smap = smappath, win_indel = 10000, perc_similarity = 0.5,returnMethod="dataFrame", EnzymeType = "SV", input_fmt_SV = "Text") datdecipher[1,] ## ----eval=TRUE---------------------------------------------------------------- path <- system.file("extdata", "Bionano_config/", package = "nanotatoR") pattern <- "*_hg19_*" smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") datbndb <- BNDBfrequency(smap = smap, buildBNInternalDB=TRUE, input_fmt_SV = "Text", dbOutput="dataframe", BNDBpath = path, BNDBpattern = pattern, fname, outpath, win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, limsize = 1000, transconf = 0.1, returnMethod=c("dataFrame"), EnzymeType = c("SE")) datbndb[1,] ## ----eval=TRUE---------------------------------------------------------------- smapName= "GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt="Text"; datInf <- internalFrequencyTrio_Duo(smap = smap, buildSVInternalDB=TRUE, win_indel=10000, win_inv_trans=50000, labelType = c("SE"), SE_path = system.file("extdata", "SoloFile/", package="nanotatoR"), SE_pattern = "*_DLE1_*", Samplecodes = system.file("extdata", "nanotatoR_sample_codes.csv", package="nanotatoR"), mergeKey = system.file("extdata", "nanotatoR_control_sample_codes.csv", package="nanotatoR"), mergedKeyoutpath = system.file("extdata", package="nanotatoR"), mergedKeyFname = "Sample_index.csv", EnzymeType = "SE", indexfile = system.file("extdata", mergedKeyFname, package="nanotatoR"), perc_similarity=0.5, indelconf=0.5, invconf=0.01, transconf=0.1, limsize=1000, win_indel_parents=5000, win_inv_trans_parents=40000, returnMethod="dataFrame", input_fmt_SV = "Text") datInf[1,] ## ----eval=TRUE---------------------------------------------------------------- smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "bed", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SE", bperrorindel = 3000, bperrorinvtrans = 50000) datcomp[1,] ## ----eval=FALSE--------------------------------------------------------------- # terms="CIRRHOSIS, FAMILIAL" # genes <- gene_list_generation( # method_entrez = c("Single"), # term = terms, # returnMethod=c("dataFrame"), # omimID = "OMIM:118980", # omim = system.file("extdata", "mim2gene.txt", package="nanotatoR"), # clinvar = system.file("extdata", "localPDB/", package="nanotatoR"), # gtr = system.file("extdata", "gtrDatabase.txt", package="nanotatoR"), # downloadClinvar = FALSE, downloadGTR = FALSE) # genes[1:10,] ## ----eval=TRUE---------------------------------------------------------------- RNASeqDir = system.file("extdata", package="nanotatoR") returnMethod="dataFrame" datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, returnMethod = returnMethod) smapName="NA12878_DLE1_VAP_solo5.smap" smap = system.file("extdata", smapName, package="nanotatoR") smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "bed", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SE", bperrorindel = 3000, bperrorinvtrans = 50000) datRNASeq1 <- SVexpression_solo (input_fmt_SV=c("dataFrame"), smapdata = datcomp, input_fmt_RNASeq=c("dataFrame"), RNASeqData = datRNASeq, outputfmt=c("datFrame"), pattern_Proband = "*_P_*", EnzymeType = c("SE")) datRNASeq1[1,] ## ----eval=TRUE---------------------------------------------------------------- smapName <- "GM24385_Ason_DLE1_VAP_trio5.smap" outputFilename <- "GM24385_Ason_DLE1_VAP_trio5_out" smappath <- system.file("extdata", smapName, package = "nanotatoR") outpath <- system.file("extdata", smapName, package = "nanotatoR") RZIPpath <- system.file("extdata", "zip.exe", package = "nanotatoR") smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") directoryName <- system.file("extdata", package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "bed", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SE", bperrorindel = 3000, bperrorinvtrans = 50000) hgpath=system.file("extdata", "GRCh37_hg19_variants_2016-05-15.txt", package="nanotatoR") datDGV <- DGVfrequency (hgpath = hgpath, smap_data = datcomp, win_indel_DGV = 10000, input_fmt_SV = "dataFrame",EnzymeType = "SE", perc_similarity_DGV = 0.5,returnMethod="dataFrame") indelconf = 0.5; invconf = 0.01;transconf = 0.1; datInf <- internalFrequencyTrio_Duo(smapdata = datDGV, buildSVInternalDB=TRUE, win_indel=10000, win_inv_trans=50000, labelType = c("SE"), EnzymeType = "SE", SE_path = system.file("extdata", "SoloFile/", package="nanotatoR"), SE_pattern = "*_DLE1_*", perc_similarity_parents =0.9, Samplecodes = system.file("extdata", "nanotatoR_sample_codes.csv", package="nanotatoR"), mergeKey = system.file("extdata", "nanotatoR_control_sample_codes.csv", package="nanotatoR"), mergedKeyoutpath = system.file("extdata", package="nanotatoR"), mergedKeyFname = "Sample_index.csv", indexfile = system.file("extdata", mergedKeyFname, package="nanotatoR"), perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, transconf = 0.1, limsize = 1000, win_indel_parents = 5000, win_inv_trans_parents=40000, returnMethod="dataFrame", input_fmt_SV = "dataFrame") path <- system.file("extdata", "Bionano_config/", package = "nanotatoR") pattern <- "*_hg19_*" datBNDB <- BNDBfrequency(smapdata = datInf, buildBNInternalDB=TRUE, input_fmt_SV = "dataFrame", dbOutput="dataframe", BNDBpath = path, BNDBpattern = pattern, fname, outpath, win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, limsize = 1000, transconf = 0.1, returnMethod=c("dataFrame"), EnzymeType = c("SE")) decipherpath = system.file("extdata", "population_cnv.txt", package="nanotatoR") datdecipher <- Decipherfrequency (decipherpath = decipherpath, smap_data = datBNDB, win_indel = 10000, perc_similarity = 0.5,returnMethod="dataFrame", input_fmt_SV = "dataFrame", EnzymeType = c("SE")) run_bionano_filter_SE_Trio (input_fmt_geneList = c("Text"), input_fmt_SV = c("dataFrame"), svData = datdecipher, dat_geneList = dat_geneList, RZIPpath = RZIPpath, EnzymeType = c("SE"), outputType = c("csv"), primaryGenesPresent = FALSE, fileprefix = "AnnotatedSamplesGM24385", outputFilename = outputFilename, directoryName = directoryName, outpath = outpath) ## ----eval=TRUE---------------------------------------------------------------- smapName="NA12878_DLE1_VAP_solo5.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") hgpath=system.file("extdata", "GRCh37_hg19_variants_2016-05-15.txt", package="nanotatoR") labelType = c("SE") SE_path = system.file("extdata", "SoloFile/", package="nanotatoR") SE_pattern = "*_DLE1_*" Samplecodes = system.file("extdata", "nanotatoR_sample_codes.csv", package="nanotatoR") mergeKey = system.file("extdata", "nanotatoR_control_sample_codes.csv", package="nanotatoR") mergedKeyoutpath = system.file("extdata", package="nanotatoR") mergedKeyFname = "Sample_index.csv" RNASeqDir = system.file("extdata", "NA12878_P_Blood_S1.genes.results", package="nanotatoR") path = system.file("extdata", "Bionano_config/", package = "nanotatoR") pattern = "_hg19.txt" outputFilename <- "NA12878_DLE1_VAP_solo5_out" outpath <- system.file("extdata", smapName, package = "nanotatoR") RZIPpath <- system.file("extdata", "zip.exe", package = "nanotatoR") directoryName <- system.file("extdata", package="nanotatoR") nanotatoR_main_Solo_SE( smap = smap, bed = bedFile, inputfmt = c("bed"), n=3, buildBNInternalDB=TRUE, path = path , pattern = pattern, buildSVInternalDB = TRUE, EnzymeType = c("SE"), labelType = c("SE"), SE_path = SE_path, SE_pattern = SE_pattern, win_indel_INF = 10000, win_inv_trans_INF = 50000, perc_similarity_INF= 0.5, indelconf = 0.5, invconf = 0.01, transconf = 0.1, hgpath = hgpath, win_indel_DGV = 10000, win_inv_trans_DGV = 50000, perc_similarity_DGV = 0.5, RNAseqcombo = TRUE, RNASeqDir = RNASeqDir, returnMethod = "dataFrame", pattern_Proband = "*_P_*", outpath = outpath, outputFilename = outputFilename, termListPresent = FALSE, datGeneListPresent = FALSE, InternaldatabasePresent = FALSE, primaryGenesPresent = FALSE, fileprefix = "AnnotatedNA12878", directoryName = directoryName, outputType = c("csv"))