BNDBfrequency: Calculates the internal frequencies of BNDB cohorts

View source: R/cohortDB_comp.r

BNDBfrequencyR Documentation

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. 3, 2024, 12:46 a.m.