internalFrequency: Calculates the internal frequencies of SV in internal cohorts

Description Usage Arguments Value Examples

View source: R/Internal_frequency.r

Description

Calculates the internal frequencies of SV in internal cohorts

Usage

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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

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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.