cohortFrequency: Calculates the internal frequencies of SV in bionano cohorts

In nanotatoR: nanotatoR: next generation structural variant annotation and classification

Description

Calculates the internal frequencies of SV in bionano cohorts

Usage

cohortFrequency(internalBNDB, smappath, smap, buildBNInternalDB = FALSE,
  smapdata, input_fmt = c("Text", "dataFrame"),
  dbOutput = c("dataframe", "text"), BNDBPath, BNDBPattern, fname,
  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"))

Arguments

internalBNDB	character. Path to the merged BN files.
smappath	character. path to the query smap file.
smap	character. File name for the smap
buildBNInternalDB	boolean. Checking whether the merged bionano file database exist.
smapdata	character. SV data in dataframe.
input_fmt	character. Choice between Text and DataFrame.
dbOutput	character. Output of merged bionano data.
BNDBPath	Path of Bionano database files.
BNDBPattern	Pattern of Bionano database files.
fname	character. Filename in case dbOutput = Text.
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 . Minimum size to consider for a SV.
transconf	Numeric. Threshold for translocation Score.
returnMethod	character. Choice between Text and DataFrame.

Value

Text file or data frames containing internalFrequency data.

Examples

mergedFiles <- system.file("extdata", "BNSOLO2_merged.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;
indelconf = 0.5; invconf = 0.01;transconf = 0.1
cohortFreq<-cohortFrequency(internalBNDB = mergedFiles , smappath , 
smap=smapName, input_fmt ="Text", 
buildBNInternalDB=FALSE, win_indel, win_inv_trans, 
perc_similarity , indelconf, invconf, 
transconf,returnMethod="dataFrame")

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