run_bionano_filter_SVMerge_Trio {nanotatoR} | R Documentation |
Getting the data from annotated smaps to extract SV information based on type of variants.
run_bionano_filter_SVMerge_Trio( input_fmt_geneList = c("Text", "dataFrame"), input_fmt_SV = c("Text", "dataFrame"), EnzymeType = c("SVMerge", "SE"), smap = NULL, svData, dat_geneList, fileName, outpath, outputFilename = "", RZIPpath, primaryGenesPresent = TRUE, outputType = c("Excel", "csv"), directoryName, fileprefix )
input_fmt_geneList |
character. Choice of gene list input Text or Dataframe. |
input_fmt_SV |
character. Choice of gene list input Text or Dataframe. |
EnzymeType |
Character. Enzyme type used. Options SVMerge or SE. |
smap |
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. |
primaryGenesPresent |
boolean Checks whether the primary gene List is present or not. |
outputType |
Character. Variants in excel tabs or in different csv files. Options Excel or csv. |
directoryName |
Character. Directory name where individual SV files will be stored. |
fileprefix |
Character. fileprefix to use for each of the files in the directory. |
Excel file containing the annotated SV map, tabs divided based on type of SVs.
## Not run: smapName <- "GM24385_DLE-1_P_trio_hg19.smap" outputFilename <- "GM24385_DLE-1_P_trio_hg19_out" smappath <- system.file("extdata", smapName, package = "nanotatoR") outpath <- system.file("extdata", smapName, package = "nanotatoR") RZIPpath <- system.file("extdata", "zip.exe", package = "nanotatoR") run_bionano_filter_SVMerge_Trio (input_fmt_geneList = c("Text"), input_fmt_SV = c("Text"), smap = smappath, dat_geneList = dat_geneList, RZIPpath = RZIPpath, EnzymeType = c("SVMerge"), outputType = c("Excel"), primaryGenesPresent = FALSE, outputFilename = outputFilename, outpath = outpath)#' ## End(Not run)