DGV_extraction: Frequency calculation of variants compared to DGV.

Description Usage Arguments Value Examples

View source: R/DGV_extraction.r

Description

Frequency calculation of variants compared to DGV.

Usage

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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

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## 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)

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