internalFrequencyTrio_Duo: Calculates the internal frequencies of SV in internal...

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

Description

Calculates the internal frequencies of SV in internal cohorts, for SVMerge

Usage

internalFrequencyTrio_Duo(
  mergedFiles,
  smappath,
  smap,
  buildSVInternalDB = FALSE,
  smapdata,
  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"),
  perc_similarity_parents = 0.9,
  returnMethod = c("Text", "dataFrame"),
  input_fmt_SV = c("Text", "dataFrame"),
  indexfile,
  EnzymeType = c("SVmerge", "SE"),
  labelType = c("SVMerge", "SE", "Both"),
  SVMerge_path,
  SVMerge_pattern,
  SE_path,
  SE_pattern,
  Samplecodes,
  mergeKey,
  mergedKeyoutpath,
  mergedKeyFname
)

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.
path	character. Path to the solo file database.
pattern	character. pattern of the file names to merge.
outpath	character. Path where the merged samples are kept.
win_indel	N umeric. 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.
perc_similarity_parents	Numeric . ThresholdPercentage similarity for zygosity determination. Default 0.9.
returnMethod	character. Choice between Text and DataFrame. Required if you want to calculate internal frequency.
input_fmt_SV	Format in which data is provided as an input to thefunction.
indexfile	File containing connection between sample and nanoIDs
EnzymeType	Character. Type of enzyme. Options Dual and DLE.
labelType	character. Type of labels used for mapping. Choices are Dual, DLE and Both.
SVMerge_path	character. Path for the Dual labelled cmap
SVMerge_pattern	character. pattern of the dual files.
SE_path	character. Path for the Dual labelled cmap
SE_pattern	character. pattern of the dual files.
Samplecodes	character. File containing relations and IDs associated to them.
mergeKey	character. File containing sample ID and relation.
mergedKeyoutpath	character. File path storing sample name and nanoID key information.
mergedKeyFname	character. File name storing sample name and nanoID key information.

Value

Calculated internal frequency in dataframe or text.

Examples

smapName="GM24385_Ason_DLE1_VAP_trio5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt_SV="Text";
datInf <- internalFrequency_solo( smap = smap, 
buildSVInternalDB = FALSE, win_indel=10000, 
win_inv_trans=50000, EnzymeType = "SE",
mergedFiles = system.file("extdata", "nanotatoRControl.txt", package="nanotatoR"), 
perc_similarity_parents =0.9,
indexfile = system.file("extdata", "Sample_index.csv", package="nanotatoR"),
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", input_fmt_SV = "Text")

VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.