merging_SE_SVMerge: Merging Dual and DLE, and adding nanotatoR relation ID

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

Merging Dual and DLE, and adding nanotatoR relation ID

Description

Merging Dual and DLE, and adding nanotatoR relation ID

Usage

merging_SE_SVMerge(
  labelType = c("SVMerge", "SE", "Both", "SE_Cancer"),
  SVMerge_path,
  SVMerge_pattern,
  SE_path,
  SE_pattern,
  Samplecodes,
  mergeKey,
  outpath,
  mergedKeyoutpath,
  mergedKeyFname,
  filename,
  outputMode = c("dataframe", "Text")
)

Arguments

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.
outpath	character. Path where the merged samples are kept.
mergedKeyoutpath	character. File path storing sample name and nanoID key information.
mergedKeyFname	character. File name storing sample name and nanoID key information.
filename	character. Output file name.
outputMode	character. Mode of databse output. Text or dataframe.

Value

Text files containg merged smaps from different samples

Examples

dat1 <- merging_SE_SVMerge (
labelType = c("SE"),
SE_path = system.file("extdata", "SoloFile/", package="nanotatoR"),
SE_pattern = "*_DLE1_*",
Samplecodes = system.file("extdata", "nanotatoR_sample_codes.csv", package="nanotatoR"),
mergeKey = system.file("extdata", "nanotatoR_control_sample_codes.csv", package="nanotatoR"),
outpath = system.file("extdata", package="nanotatoR"),
mergedKeyoutpath = system.file("extdata", package="nanotatoR"), 
mergedKeyFname = "Sample_index.csv",
filename= "nanotatoRControl.txt", 
outputMode = "dataframe")

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.