Description Usage Arguments Value Examples
Fusions handler_data filter that can be used to prepare the input data for downstream analysis
1 2 3 4 5 6 7 8 | fusions_filter(input_data, input_type = "common",
config_file = system.file("extdata", "config/filter.toml", package =
"ngstk"), config_list = NULL,
handler_confg_file = system.file("extdata", "config/handler.toml",
package = "ngstk"), mhandler_confg_file = system.file("extdata",
"config/mhandler.toml", package = "ngstk"), handler_funs = NULL,
mhandler_funs = NULL, handler_extra_params = NULL,
mhandler_extra_params = NULL, outfn = NULL)
|
input_data |
A data frame containing the fusions cols (gene5, gene3, fusion_type) |
input_type |
Fusion filter type |
config_file |
ngstk filter configuration file path, default is system.file('extdata', 'config/filter.toml', package = 'ngstk') |
config_list |
ngstk filter configuration, default is NULL and read from config_file |
handler_confg_file |
ngstk handler configuration file path, default is system.file('extdata', 'config/handler.toml', package = 'ngstk') |
mhandler_confg_file |
ngstk handler configuration file path, default is system.file('extdata', 'config/mhandler.toml', package = 'ngstk') |
handler_funs |
handler function for single colnum, default is NULL and get value from config_file |
mhandler_funs |
handler function for mulitple colnums, #' default is NULL and get value from config_file |
handler_extra_params |
Extra parameters pass to handler |
mhandler_extra_params |
Extra parameters pass to mhandler system.file('extdata', 'config/filter.toml', package = 'ngstk') |
outfn |
Default is NULL and not output the result to file |
A data frame
1 2 3 4 | demo_file <- system.file('extdata',
'demo/proteinpaint/fusions2pp_fusioncatcher.txt', package = 'ngstk')
input_data <- read.table(demo_file, sep = '\t', header = TRUE, stringsAsFactors = FALSE)
result <- fusions_filter(input_data)
|
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