Decipherfrequency: Frequency calculation of variants compared to Decipher.

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

Frequency calculation of variants compared to Decipher.

Description

Frequency calculation of variants compared to Decipher.

Usage

Decipherfrequency(
  decipherpath,
  smap,
  smap_data,
  win_indel = 10000,
  perc_similarity = 0.5,
  returnMethod = c("Text", "dataFrame"),
  input_fmt_SV = c("Text", "dataFrame"),
  EnzymeType = c("SVMerge", "SE"),
  outpath
)

Arguments

decipherpath	character. Decipher Text file.
smap	character Filepath for smap.
smap_data	Dataset containing smap data.
win_indel	character indel window. Default 10000.
perc_similarity	Numeric . ThresholdPercentage similarity of the query SV and reference SV.
returnMethod	character. Choice between text or data frame as the output.
input_fmt_SV	boolean . Options SE and SVMerge.
EnzymeType	boolean . Options SE and SVMerge.
outpath	character. Path where gene lists are saved.

Value

dataframe containing decipher data. are stored as text files.

Examples

decipherpath = system.file("extdata", "population_cnv.txt",
package="nanotatoR")
smappath=system.file("extdata", "GM24385_Ason_DLE1_VAP_trio5.smap", 
package="nanotatoR")
datdecipher <- Decipherfrequency (decipherpath = decipherpath, 
smap = smappath, win_indel = 10000,
EnzymeType= "SE",
perc_similarity = 0.5,returnMethod="dataFrame", 
input_fmt_SV = "Text")
datdecipher[1,]

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