nanotatoR_main_Trio_SE: Annotation and visualisation of Bionano SV, of DLE Trio...

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Description

Annotation and visualisation of Bionano SV, of DLE Trio samples.

Usage

nanotatoR_main_Trio_SE(
  smap,
  bed,
  inputfmtBed = c("bed", "BNBed"),
  n = 3,
  buildBNInternalDB = TRUE,
  mergedFiles,
  smappath,
  buildSVInternalDB = FALSE,
  path,
  pattern,
  win_indel_INF = 10000,
  win_inv_trans_INF = 50000,
  perc_similarity_INF = 0.5,
  indelconf = 0.5,
  invconf = 0.01,
  transconf = 0.1,
  perc_similarity_INF_parents = 0.9,
  hgpath,
  win_indel_DGV = 10000,
  win_inv_trans_DGV = 50000,
  perc_similarity_DGV = 0.5,
  method_entrez = c("Single", "Multiple", "Text"),
  termPath,
  term,
  thresh = 5,
  limsize = 1000,
  EnzymeType = c("SVmerge", "SE"),
  labelType = c("SVMerge", "SE", "Both"),
  SVMerge_path,
  SVMerge_pattern,
  SE_path,
  SE_pattern,
  Samplecodes,
  mergeKey,
  mergedKeyoutpath,
  mergedKeyFname,
  RNAseqcombo = TRUE,
  RNASeqDir,
  returnMethod = "dataFrame",
  RNASeqData,
  RNASeqPATH,
  pattern_Proband = NA,
  pattern_Mother = NA,
  pattern_Father = NA,
  outpath,
  outputFilename = "",
  termListPresent = TRUE,
  internalBNDB,
  clinvar,
  InternaldatabasePresent = TRUE,
  RNASeqDatasetPresent = TRUE,
  geneListPresent = TRUE,
  omim,
  gtr,
  removeClinvar = FALSE,
  removeGTR = FALSE,
  downloadClinvar = FALSE,
  downloadGTR = FALSE,
  url_gtr,
  omimID,
  RZIPpath,
  directoryName,
  fileprefix,
  datGeneListPath,
  decipherpath,
  indexfile,
  primaryGenesPresent = TRUE,
  outputType = c("Excel", "csv")
)

Arguments

smap	character. File name for the smap
bed	Text Bionano Bed file.
inputfmtBed	character Whether the bed input is UCSC bed or Bionano bed.
n	numeric Number of genes to report which are nearest to the breakpoint. Default is 3.
buildBNInternalDB	boolean. Checking whether the merged BNDB file database exist.
mergedFiles	character. Path to the merged SV files.
smappath	character. Path and file name for textfile.
buildSVInternalDB	boolean. Checking whether the merged solo file database exist.
path	character. Path to the solo file database.
pattern	character. pattern of the file names to merge.
win_indel_INF	Numeric. Insertion and deletion error window.
win_inv_trans_INF	Numeric. Inversion and translocation error window.
perc_similarity_INF	Numeric . ThresholdPercentage similarity of the query SV and reference SV.
indelconf	Numeric. Threshold for insertion and deletion confidence.
invconf	Numeric. Threshold for inversion confidence.
transconf	Numeric. Threshold for translocation confidence.
perc_similarity_INF_parents	Numeric . ThresholdPercentage similarity for parent zygosity calculation. Default threshold 0.9.
hgpath	character. Path to Database of Genomic Variants (DGV) Text file.
win_indel_DGV	Numeric. Insertion and deletion error window for DGV.
win_inv_trans_DGV	Numeric. Inversion and translocation error window for DGV.
perc_similarity_DGV	Numeric . ThresholdPercentage similarity of the query SV and reference SV, for DGV..
method_entrez	character. Input Method for terms. Choices are "Single","Multiple" and "Text".
termPath	character. Path and file name for textfile.
term	character. Single or Multiple Terms.
thresh	integer. Threshold for the number of terms sent to entrez. Note if large lists are sent to ncbi, it might fail to get processed. Default is 5.
limsize	Numeric. Minimum size for SV. Default 1000.
EnzymeType	Character. Type of enzyme. Options Dual and DLE.
labelType	character. Type of labels used for mapping. Choices are Dual, DLE and Both.
SVMerge_path	character. Path for the Dual labelled cmap
SVMerge_pattern	character. pattern of the dual files.
SE_path	character. Path for the Dual labelled cmap
SE_pattern	character. pattern of the dual files.
Samplecodes	character. File containing relations and IDs associated to them.
mergeKey	character. File containing sample ID and relation.
mergedKeyoutpath	character. File path storing sample name and nanoID key information.
mergedKeyFname	character. File name storing sample name and nanoID key information.
RNAseqcombo	boolean whether RNASeq datasets are combined or not.
RNASeqDir	boolean Directory for RNASeq.
returnMethod	character. Choice between text or data frame as the output.
RNASeqData	dataFrame. RNAseq data with gene names.
RNASeqPATH	character. RNAseq dataset path .
pattern_Proband	character. Pattern for proband.
pattern_Mother	character. Pattern to identify the mother reads.
pattern_Father	character. Pattern to identify the father reads.
outpath	Character Directory to the output file.
outputFilename	Character Output filename.
termListPresent	logical Checks whether term list is provided by the user.
internalBNDB	character. internak Bionano merged databse.
clinvar	character. clinvar file name and location.
InternaldatabasePresent	boolean. Checking whether internal DB present.
RNASeqDatasetPresent	boolean. Checking whether RNASeq database present or not.
geneListPresent	logical Checks whether gene list is provided by the user.
omim	character. omim2gene file name and location.
gtr	character. gtr file name and location.
removeClinvar	logical. Deletes the Clinvar database if TRUE.
removeGTR	logical. Deletes the GTR database if TRUE.
downloadClinvar	logical. Downloads the Clinvar database if TRUE.
downloadGTR	logical. Downloads the GTR database if TRUE.
url_gtr	character. url for GTR.
omimID	character. Omim ID.
RZIPpath	character. Path to RZippath.
directoryName	Directory name where individual SV files will be stored.
fileprefix	character Prefix to use for each of the files in the directory.
datGeneListPath	Character Path for genelist.
decipherpath	character. Decipher database path.
indexfile	character. indexfile containing nano ID and sample relation.
primaryGenesPresent	logical Checks whether primarygene list is provided by the user.
outputType	Variants in excel tabs or in different csv files. Options Excel or csv.

Value

Excel file containing the annotated SV map, tabs divided based on type of SVs.

Text files containg gene list and terms associated with them are stored as text files.

Examples

smapName="GM24385_Ason_DLE1_VAP_trio5.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")
decipherpath = system.file("extdata", "population_cnv.txt", package="nanotatoR")
omim = system.file("extdata", "mim2gene.txt", package="nanotatoR") 
clinvar = system.file("extdata", "localPDB/", package="nanotatoR") 
gtr = system.file("extdata", "gtrDatabase.txt", package="nanotatoR")
mergedFiles = system.file("extdata", "nanotatoRControl.txt", package="nanotatoR")
indexfile = system.file("extdata", "Sample_index.csv", package="nanotatoR")
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")
nanotatoR_main_Trio_SE(
smap = smap, bed = bedFile, inputfmtBed = c("bed"), 
n=3,EnzymeType = c("SE"),
buildBNInternalDB=TRUE,
 path = path , pattern = pattern, 
buildSVInternalDB = FALSE,
decipherpath = decipherpath,
win_indel_INF = 10000, win_inv_trans_INF = 50000, 
perc_similarity_INF= 0.5, indelconf = 0.5, invconf = 0.01, 
transconf = 0.1, perc_similarity_INF_parents = 0.9,
hgpath = hgpath, win_indel_DGV = 10000, 
win_inv_trans_DGV = 50000, 
perc_similarity_DGV = 0.5, limsize = 1000,
method_entrez=c("Single"), 
term = "Liver cirrhosis", RZIPpath = RZIPpath,
omim = omim, clinvar = clinvar, gtr = gtr, 
removeClinvar = TRUE, removeGTR = TRUE, 
downloadClinvar = FALSE, downloadGTR = FALSE,
RNASeqDatasetPresent = TRUE,
RNAseqcombo = TRUE, geneListPresent = FALSE,
RNASeqDir = RNASeqDir, returnMethod = "dataFrame",
pattern_Proband = "*_P_*",
outpath = outpath,
indexfile = system.file("extdata", "Sample_index.csv",package="nanotatoR"),
primaryGenesPresent = FALSE,
outputFilename = outputFilename, 
termListPresent = FALSE,
InternaldatabasePresent = TRUE,
outputType = c("Excel"))

VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.