DGV_extraction: Frequency calculation of variants compared to DGV.

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

Description

Frequency calculation of variants compared to DGV.

Usage

DGV_extraction(hgpath, smappath, smap, smap_data,
  input_fmt_DGV = c("Text", "dataFrame"), win_indel_DGV = 10000,
  win_inv_trans_DGV = 50000, perc_similarity_DGV = 0.5,
  returnMethod = c("Text", "dataFrame"), outpath, usample = 54946)

Arguments

hgpath	character. Path to Database of Genomic Variants (DGV) Text file.
smappath	character. Path for smap textfile.
smap	character. File name for smap textfile.
smap_data	dataframe. Dataset containing smap data.
input_fmt_DGV	character. Choice between text or data frame as an input to the DGV frequency calculator.
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.
returnMethod	character. Choice between text or data frame as the output.
outpath	character. Path where gene lists are saved.
usample	Numeric. Number of unique samples.

Value

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

Examples

## Not run: 
smap <- "F1.1_TestSample1_solo_hg19.smap"
smappath <- system.file("extdata",  package = "nanotatoR")
hgpath <- system.file("extdata", "GRCh37_hg19_variants_2016-05-15.txt", 
package = "nanotatoR")
win_indel_DGV=10000;win_inv_trans_DGV=50000;perc_similarity_DGV=0.5;
usample = 54946
dgv <- DGV_extraction (hgpath, input_fmt_DGV = "Text",smap=smap, 
smappath, win_indel_DGV = 10000, win_inv_trans_DGV = 50000,
perc_similarity_DGV = 0.5,returnMethod="dataFrame",usample = 54946)

## End(Not run)

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