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

View source: R/mergesmap_SVMerge_SE.R

merging_SE_SVMergeR Documentation

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.