BNDBfrequency: Calculates the internal frequencies of BNDB cohorts

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

Calculates the internal frequencies of BNDB cohorts

Description

Calculates the internal frequencies of BNDB cohorts

Usage

BNDBfrequency(
  internalBNDB,
  smappath,
  smap,
  buildBNInternalDB = FALSE,
  smapdata,
  input_fmt_SV = c("Text", "dataFrame"),
  dbOutput = c("dataframe", "text"),
  BNDBpath,
  BNDBpattern,
  outpath,
  win_indel = 10000,
  win_inv_trans = 50000,
  perc_similarity = 0.5,
  indelconf = 0.5,
  invconf = 0.01,
  limsize = 1000,
  transconf = 0.1,
  returnMethod = c("Text", "dataFrame"),
  EnzymeType = c("SVmerge", "SE")
)

Arguments

internalBNDB	character. Path to the merged SV files.
smappath	character. path to the query smap file.
smap	character. File name for the smap
buildBNInternalDB	boolean. Checking whether the merged BNDB file database exist.
smapdata	dataframe. smapdata in the form of dataframe.
input_fmt_SV	character. Choice between Text and DataFrame.
dbOutput	character. database output type. Options dataframe or text.
BNDBpath	character. Path to the BNDB file database.
BNDBpattern	character. pattern of the file names to merge.
outpath	character. Path to merged SV solo datasets.
win_indel	Numeric. Insertion and deletion error window.
win_inv_trans	Numeric. Inversion and translocation error window.
perc_similarity	Numeric . ThresholdPercentage similarity of the query SV and reference SV.
indelconf	Numeric. Threshold for insertion and deletion Score.
invconf	Numeric. Threshold for inversion Score.
limsize	Numeric. SV size limit.
transconf	Numeric. Threshold for translocation Score.
returnMethod	character. Choice between Text and DataFrame.
EnzymeType	Character. Type of enzyme. Options SVmerge and SE.

Value

Text file or data frames containing internalFrequency data.

Examples

path <- system.file("extdata", "Bionano_config/", package = "nanotatoR")
pattern <- "*_hg19_*"
smapName="GM24385_Ason_DLE1_VAP_trio5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
BNDBfrequency(smap = smap, 
 buildBNInternalDB=TRUE, 
   input_fmt_SV = "Text",
   dbOutput="dataframe",
   BNDBpath = path, 
   BNDBpattern = pattern, 
   outpath, 
   win_indel = 10000,
   win_inv_trans = 50000, 
 perc_similarity = 0.5, 
   indelconf = 0.5, 
   invconf = 0.01, 
   limsize = 1000,
 transconf = 0.1,
   returnMethod=c("dataFrame"), 
   EnzymeType = c("SE"))

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