run_bionano_filter {nanotatoR}R Documentation

Getting the data from annotated smaps to extract SV information based on type of variants.

Description

Getting the data from annotated smaps to extract SV information based on type of variants.

Usage

run_bionano_filter(input_fmt_geneList = c("Text", "dataFrame"),
  input_fmt_svMap = c("Text", "dataFrame"), SVFile = NULL, svData,
  dat_geneList, fileName, outpath, outputFilename = "", RZIPpath)

Arguments

input_fmt_geneList

character. Choice of gene list input Text or Dataframe.

input_fmt_svMap

character. Choice of gene list input Text or Dataframe.

SVFile

character. SV file name.

svData

Dataframe Input data containing SV data.

dat_geneList

Dataframe Input data containing geneList data.

fileName

Character Name of file containing Gene List data.

outpath

Character Directory to the output file.

outputFilename

Character Output filename.

RZIPpath

Character Path for the Rtools Zip package.

Value

Excel file containing the annotated SV map, tabs divided based on type of SVs.

Examples

## Not run: 
terms <- "Muscle Weakness"
gene <- gene_list_generation(
  method = "Single", term = terms,
  returnMethod_GeneList = "dataFrame"
)
RzipFile = "zip.exe"
RZIPpath <- system.file("extdata", RzipFile, package = "nanotatoR")
smapName <- "F1.1_TestSample1_solo_hg19.smap"
smappath <- system.file("extdata", smapName, package = "nanotatoR")
smappath1 <- system.file("extdata", package = "nanotatoR")
run_bionano_filter(input_fmt_geneList = c("dataframe"), input_fmt_svMap = c("Text"),
  SVFile = smappath, dat_geneList = gene, outpath = smappath1, outputFilename = "test", 
  RZIPpath = RZIPpath)

## End(Not run)

[Package nanotatoR version 1.8.0 Index]