View source: R/filterread_Trio_SVMerge.r
run_bionano_filter_SVMerge_Trio | 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)
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