Description Usage Arguments Value Examples
View source: R/cbioportal_trasefer.R
Function to convert mutation data to cbioportal Oncoprinter format.
1 2 3 4 5 6 7 8 | muts2oncoprinter(input_data, input_type = "iseq",
config_file = system.file("extdata", "config/cbioportal.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 mutation data.frame need to be converted to ProteinPaint input. |
input_type |
Point the input data format (iseq or others) |
config_file |
ngstk ProteinPaint configuration file path, default is system.file('extdata', 'config/proteinpaint.toml', package = 'ngstk') |
config_list |
ngstk ProteinPaint 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 |
outfn |
Default is NULL and not output the result to file |
A data frame
1 2 3 4 5 6 7 | demo_file <- system.file('extdata',
'demo/proteinpaint/muts2pp_iseq.txt', package = 'ngstk')
input_data <- read.table(demo_file, sep = '\t', header = TRUE, stringsAsFactors = FALSE)
disease <- 'T-ALL'
input_data <- data.frame(input_data, disease)
input_data$disease <- as.character(input_data$disease)
muts2oncoprinter(input_data, input_type = 'iseq')
|
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