run_bionano_filter_SE_Trio {nanotatoR} | R Documentation |
Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SE_Trio( primaryGenesPresent = TRUE, input_fmt_geneList = c("Text", "dataFrame"), input_fmt_SV = c("Text", "dataFrame"), smap = NULL, svData, dat_geneList, fileName, outpath, outputFilename = "", RZIPpath, outputType = c("Excel", "csv"), directoryName, fileprefix, EnzymeType = c("SVMerge", "SE") )
primaryGenesPresent |
boolean Checks whether the primary gene List is present or not. |
input_fmt_geneList |
character. Choice of gene list input Text or Dataframe. |
input_fmt_SV |
character. Choice of gene list input Text or Dataframe. |
smap |
character. SV file name. |
svData |
Dataframe Input data containing SV data. |
dat_geneList |
Dataframe Input data containing geneList data. |
fileName |
Character Name of file containing Gene List data. |
outpath |
Character Directory to the output file. |
outputFilename |
Character Output filename. |
RZIPpath |
Character Path for the Rtools Zip package. |
outputType |
Character. Variants in excel tabs or in different csv files. Options Excel or csv. |
directoryName |
Character. Directory name where individual SV files will be stored. |
fileprefix |
Character. fileprefix to use for each of the files in the directory. |
EnzymeType |
Character. Enzyme type used. Options SVmerge or SE. |
Excel file containing the annotated SV map, tabs divided based on type of SVs.
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, directoryName = directoryName, fileprefix = "AnnotatedSamplesGM24385")