run_bionano_filter: Getting the data from annotated smaps to extract SV...

In nanotatoR: nanotatoR: next generation structural variant annotation and classification

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)

nanotatoR documentation built on Nov. 8, 2020, 6:54 p.m.