DGVfrequency: Frequency calculation of variants compared to DGV.

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

Frequency calculation of variants compared to DGV.

Description

Frequency calculation of variants compared to DGV.

Usage

DGVfrequency(
  hgpath,
  smap,
  smap_data,
  win_indel_DGV = 10000,
  win_inv_trans_DGV = 50000,
  perc_similarity_DGV = 0.5,
  input_fmt_SV = c("Text", "dataframe"),
  returnMethod = c("Text", "dataFrame"),
  outpath,
  EnzymeType = c("SVMerge", "SE")
)

Arguments

hgpath	character. Path to Database of Genomic Variants (DGV) Text file.
smap	character. File name for smap textfile.
smap_data	dataframe. Dataset containing smap data.
win_indel_DGV	Numeric. Insertion and deletion error window.Default 10000 bases.
win_inv_trans_DGV	Numeric. Inversion and translocation error window. Default 50000 bases.
perc_similarity_DGV	Numeric . ThresholdPercentage similarity of the query SV and reference SV. Default 0.5.
input_fmt_SV	boolean . Options Text and dataframe.
returnMethod	character. Choice between text or data frame as the output.
outpath	character. Path where gene lists are saved.
EnzymeType	boolean . Options SE and SVMerge.

Value

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

Examples

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,
win_indel_DGV = 10000,
EnzymeType = "SE", 
input_fmt_SV = "Text",
perc_similarity_DGV = 0.5,returnMethod="dataFrame")

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.