Decipher_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

Decipher_extraction(decipherpath, smappath, smap, smap_data,
  input_fmt = c("Text", "dataFrame"), win_indel = 10000,
  perc_similarity = 0.5, returnMethod = c("Text", "dataFrame"))

Arguments

decipherpath	character. Path to DECIPHER Text file.
smappath	character. path to the query smap file.
smap	character. File name for the smap.
smap_data	character. Dataframe if input type chosen as dataframe.
input_fmt	character. Choice between text or data frame as an input to the DGV frequency calculator.
win_indel	Numeric. Insertion and deletion error window. Default 10000.
perc_similarity	Numeric . ThresholdPercentage similarity of the query SV and reference SV. Default 0.5.
returnMethod	character. Choice between text or data frame as the output.

Value

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

Examples

decipherpath <- system.file("extdata", "population_cnv.txt", 
package = "nanotatoR")
smapName <- "F1.1_TestSample1_solo_hg19.smap"
smappath <- system.file("extdata", package = "nanotatoR")
win_indel=10000;win_inv_trans=50000;perc_similarity=0.5
decipherext<-Decipher_extraction (decipherpath, input_fmt = "Text", smappath, 
smap= smapName,
win_indel = 10000, perc_similarity = 0.5, returnMethod="dataFrame")

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