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

View source: R/InternalFrequency_SE.r

internalFrequency_soloR Documentation

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

Description

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

Usage

internalFrequency_solo(
  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"),
  input_fmt_SV = c("Text", "dataFrame"),
  indexfile,
  perc_similarity_parents = 0.9,
  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.

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 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.

returnMethod

character. Choice between Text and DataFrame. Required if you want to calculate internal frequency.

input_fmt_SV

character. Choice between Text and DataFrame.

indexfile

File containing connection between sample and nanoIDs

perc_similarity_parents

Numeric . ThresholdPercentage similarity for zygosity determination. Default 0.9.

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 = "NA12878_DLE1_VAP_solo5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt="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 Aug. 2, 2024, 8:45 p.m.