Function to convert mutation data to ProteinPaint https://pecan.stjude.org/pp input format.

muts2pp(input_data, input_type = "iseq",
  config_file = system.file("extdata", "config/proteinpaint.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)

Arguments

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

Value

A data frame

Examples

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) muts2pp(input_data, input_type = 'iseq')
#> gene refseq chromosome start aachange class disease #> 1 IDH1 NM_001282386 chr2 209113113 p.R132S missense T-ALL #> 2 PTPRC NM_080921 chr1 198711362 p.A694T missense T-ALL #> 3 PTPRC NM_080921 chr1 198685843 p.I281fs frameshift T-ALL #> 4 ASPM NM_001206846 chr1 197093449 p.L1061F missense T-ALL #> 5 ASPM NM_018136 chr1 197070987 p.Q2465R missense T-ALL #> 6 FAT1 NM_005245 chr4 187630354 p.L210F missense T-ALL #> 7 FAT1 NM_005245 chr4 187521292 p.H3955Y missense T-ALL #> 8 GNB4 NM_021629 chr3 179132832 p.H91delinsSH proteinIns T-ALL #> 9 KMT2C NM_170606 chr7 151900067 p.Y1348X nonsense T-ALL #> 10 KMT2C NM_170606 chr7 151879381 p.P1855L missense T-ALL #> 11 KMT2C NM_170606 chr7 151878550 p.S2132F missense T-ALL #> 12 KMT2C NM_170606 chr7 151856070 p.R3850X nonsense T-ALL #> 13 EZH2 NM_001203249 chr7 148511184 p.T517I missense T-ALL #> 14 EZH2 NM_001203249 chr7 148507443 p.L615delinsDL proteinIns T-ALL #> 15 EZH2 NM_001203249 chr7 148507439 p.F616delinsCL proteinIns T-ALL #> 16 EZH2 NM_001203249 chr7 148506474 p.V624M missense T-ALL #> 17 EZH2 NM_001203249 chr7 148506462 p.R628C missense T-ALL #> 18 EZH2 NM_001203249 chr7 148506443 p.R634H missense T-ALL #> 19 NOTCH1 NM_017617 chr9 139391015 p.M2392fs frameshift T-ALL #> 20 NOTCH1 NM_017617 chr9 139391014 p.Q2393X nonsense T-ALL #> 21 NOTCH1 NM_017617 chr9 139390805 p.P2462fs frameshift T-ALL #> 22 NOTCH1 NM_017617 chr9 139390792 p.S2467fs frameshift T-ALL #> 23 NOTCH1 NM_017617 chr9 139390791 p.S2467X nonsense T-ALL #> sample #> 1 A1 #> 2 A2 #> 3 A3 #> 4 A4 #> 5 A5 #> 6 A6 #> 7 A7 #> 8 A8 #> 9 A9 #> 10 A10 #> 11 A11 #> 12 A12 #> 13 A13 #> 14 A14 #> 15 A15 #> 16 A16 #> 17 A17 #> 18 A18 #> 19 A19 #> 20 A20 #> 21 A21 #> 22 A22 #> 23 A23