nanotatoR_main: Annotation of Bionano SV.

Description Usage Arguments Value

View source: R/mainAnnotator.r

Description

Annotation of Bionano SV.

Usage

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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.


VilainLab/Nanotator documentation built on May 20, 2019, 5:41 p.m.