run_bionano_filter {nanotatoR} | R Documentation |
Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter(input_fmt_geneList = c("Text", "dataFrame"), input_fmt_svMap = c("Text", "dataFrame"), SVFile = NULL, svData, dat_geneList, fileName, outpath, outputFilename = "", RZIPpath)
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. |
Excel file containing the annotated SV map, tabs divided based on type of SVs.
## 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)