nanotatoR_main: Annotation of Bionano SV.

In nanotatoR: nanotatoR: next generation structural variant annotation and classification

Description

Annotation of Bionano SV.

Usage

nanotatoR_main(smap, bed, inputfmtBed = c("BED", "BNBED"), n = 3,
  InternalDBpath, InternalDBpattern, dbOutput_Int, fname_Int, dbOutput_BN,
  fname_BN, buildSVInternalDB = FALSE, soloPath, solopattern,
  returnMethod_bedcomp = c("Text", "dataFrame"), mergedFiles_BN,
  win_indel_INF = 10000, win_inv_trans_INF = 50000,
  perc_similarity_INF = 0.5, indelconf = 0.5, invconf = 0.01,
  transconf = 0.1, returnMethod_DGV = c("Text", "dataFrame"), hgpath,
  win_indel_DGV = 10000, win_inv_trans_DGV = 50000,
  perc_similarity_DGV = 0.5, returnMethod_Internal = c("Text",
  "dataFrame"), input_fmt_DGV = c("Text", "dataFrame"),
  input_fmt_BN = c("Text", "dataFrame"), input_fmt_INF = c("Text",
  "dataFrame"), input_fmt_decipher = c("Text", "dataFrame"),
  input_fmt_svMap = c("Text", "dataFrame"), dat_geneList, decipherpath,
  input_fmt_geneList = c("Text", "dataFrame"),
  returnMethod_GeneList = c("Text", "dataFrame"),
  buildBNInternalDB = FALSE, returnMethod_BNCohort = c("Text",
  "dataFrame"), mergedFiles_INF, returnMethod_decipher = c("Text",
  "dataFrame"), method_entrez = c("Single", "Multiple", "Text"),
  smapName, termPath, term, thresh = 5, limsize = 1000,
  win_indel_parents = 5000, win_inv_trans_parents = 40000, outpath,
  outputFilename = "", RZIPpath)

Arguments

smap	character. Path to SMAP file.
bed	Text Choice between UCSC bed or Bionano bed.
inputfmtBed	character. Choice between Text and DataFrame as input for bed file.
n	numeric Number of genes to report which are nearest to the breakpoint. Default is 3.
InternalDBpath	character. Path to the BNFile file database.
InternalDBpattern	character. pattern of the BNFile names to merge.
dbOutput_Int	character. Output of solo bionano data.
fname_Int	character. Filename in case dbOutput_Int = Text.
dbOutput_BN	character. Output of merged bionano data.
fname_BN	character. Filename in case dbOutput_BN = Text.
buildSVInternalDB	boolean. Checking whether the merged solo file database exist or you need to build it. Default= TRUE.
soloPath	character. Path to the solo file database.
solopattern	character. pattern of the file names to merge.
returnMethod_bedcomp	character. Return Methods from the compSmapbed function, choice between Text and Dataframe.
mergedFiles_BN	character. Path to the merged BN SV files.
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.
returnMethod_DGV	character. Return Methods from the DGV_extraction function, choice between Text and Dataframe.
hgpath	character. Path to Database of Genomic Variants (DGV) Text file.
win_indel_DGV	Numeric. Insertion and deletion error window.
win_inv_trans_DGV	Numeric. Inversion and translocation error window.
perc_similarity_DGV	Numeric . ThresholdPercentage similarity of the query SV and reference SV.
returnMethod_Internal	character. Return Methods from the internalFrequency function, choice between Text and Dataframe.
input_fmt_DGV	character. Choice between Text and DataFrame for input to DGV.
input_fmt_BN	character. Choice of Bionano dataset input Text or Dataframe.
input_fmt_INF	character. Choice between Text and DataFrame for input to INF.
input_fmt_decipher	character. Choice of gene list input Text or Dataframe.
input_fmt_svMap	character. Choice of SVmap input for final step Text or Dataframe.
dat_geneList	Dataframe Input data containing geneList data.
decipherpath	character. Path to DECIPHER. Text file.
input_fmt_geneList	character. Choice of gene list input Text or Dataframe.
returnMethod_GeneList	character. Return Methods from the gene_list_generation function, choice between Text and Dataframe.
buildBNInternalDB	boolean. Checking whether the merged Bionano file database exist or you need to build it. Default= TRUE.
returnMethod_BNCohort	character. Return Methods from the Bionano function, choice between Text and Dataframe.
mergedFiles_INF	character. Path to the merged BN SV files.
returnMethod_decipher	character. Return Methods from the decipher Frequency function, choice between Text and Dataframe.
method_entrez	character. Input Method for terms for entrez. Choices are "Single","Multiple" and "Text".
smapName	character. Name of the smap file.
termPath	character. Path and file name for textfile for terms.
term	character. Single or Multiple Terms as vectord.
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 of SV that can be determined accurately by the Bionano SV caller. Default 1000.
win_indel_parents	Numeric. Insertion and deletion error window to determine zygosity in case of parents. Default 5000.
win_inv_trans_parents	Numeric. Inversion and translocation error window to determine zygosity in case of parents. Default 40000.
outpath	Character Directory to the output file.
outputFilename	Character Output filename for the annotated smap.
RZIPpath	Character. Path for the Rtools zip.exe

Value

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

nanotatoR documentation built on Nov. 8, 2020, 6:54 p.m.