internalFrequency: Calculates the internal frequencies of SV in internal cohorts

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

Description

Calculates the internal frequencies of SV in internal cohorts

Usage

internalFrequency(mergedFiles, smappath, smap, buildSVInternalDB = FALSE,
  smapdata, input_fmt = c("Text", "dataFrame"), path, pattern, outpath,
  win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5,
  indelconf = 0.5, invconf = 0.01, fname, limsize = 1000,
  win_indel_parents = 5000, win_inv_trans_parents = 40000,
  transconf = 0.1, dbOutput = c("dataframe", "text"),
  returnMethod = c("Text", "dataFrame"))

Arguments

mergedFiles	character. Path to the merged SV files.
smappath	character. path to the query smap file.
smap	character. File name for the smap
buildSVInternalDB	boolean. Checking whether the merged solo file database exist.
smapdata	character. Dataframe if input type chosen as dataframe.
input_fmt	Format in which data is provided as an input to the function.
path	character. Path to the solo file database.
pattern	character. pattern of the file names to merge.
outpath	character. Path to merged SV solo datasets.
win_indel	Numeric. Insertion and deletion error window. Default 10000.
win_inv_trans	Numeric. Inversion and translocation error window. Default 50000.
perc_similarity	Numeric . ThresholdPercentage similarity of the query SV and reference SV. Default 0.5.
indelconf	Numeric. Threshold for insertion and deletion confidence. Default 0.5
invconf	Numeric. Threshold for inversion confidence.Default 0.01.
fname	character. Filename in case dbOutput = Text.
limsize	Numeric. Minimum size of SV that can be determined acurately by the Bionano SV caller. Default 1000.
win_indel_parents	Numeric. Insertion and deletion error window to determine zygosity in case of parents. Default 5000.
win_inv_trans_parents	Numeric. Inversion and translocation error window to determine zygosity in case of parents. Default 40000.
transconf	Numeric. Threshold for translocation confidence. Default 0.1.
dbOutput	character. Output of merged bionano data.
returnMethod	character. Choice between Text and DataFrame.

Value

Text file or data frames containing internalFrequency data.

Examples

mergedFiles <- system.file("extdata", "nanotatoR_merged.txt", package = "nanotatoR")
smapName <- "F1.1_TestSample1_solo_hg19.smap"
smappath <- system.file("extdata", package = "nanotatoR")
indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt="Text";
internalFrequency(mergedFiles = mergedFiles, smappath = smappath , smap = smapName, 
buildSVInternalDB=FALSE, win_indel=10000, 
win_inv_trans=50000, 
perc_similarity=0.5, indelconf=0.5, invconf=0.01, 
transconf=0.1, limsize=1000, win_indel_parents=5000,input_fmt="Text",
win_inv_trans_parents=40000,
returnMethod="dataFrame")

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