# Next-Generation Sequencing (NGS) Data Analysis Toolkit

## Documentation for package ‘ngstk’ version 0.2.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ngstk-package | ngstk can be used to facilitate the analysis of NGS data, such as visualization, conversion of data format for WEB service input and other purpose.
batch_file | Process the input file a batch of one batch
format_filenames | Function to format filenames that can be used to unify the filenames style for more easily download or use
format_pp_meta_age | To format ProteinPaint input meta data of age
format_pp_meta_fusions | To format ProteinPaint input meta data of gender
format_pp_meta_gender | To format ProteinPaint input meta data of gender
fusions2oncoprinter | Function to convert fusion data to cbioportal Oncoprinter format.
fusions2pp | Function to convert fusion data to ProteinPaint format.
fusions2pp_meta | Function to convert fusion data to ProteinPaint heatmap meta rows format.
fusions_filter | Fusions handler_data filter that can be used to prepare the input data for downstream analysis
get_files_ctime | Function to check file create time and according the requirement to return check value
get_files_mtime | Function to check file last change time and according the requirement to return check value
get_pp_samplegroup | Function to get samplegroup file that can be pass to Proteinpaint
get_split_seqs | Function to calculate the split regions by sections and total numbers
make_option | Functions to enable our OptionParser to recognize specific command line options (optparse).
merge_table_files | Util function to merge multiple table files.
muts2mutation_mapper | Function to convert mutation data to cbioportal MutationMapper format.
muts2oncoprinter | Function to convert mutation data to cbioportal Oncoprinter format.
muts2pp | Function to convert mutation data to ProteinPaint format.
ngstk | ngstk can be used to facilitate the analysis of NGS data, such as visualization, conversion of data format for WEB service input and other purpose.
opt_parser | A function to create an instance of a parser object with subcommands.
parse_args | Parse command line options (optparse).
parse_args2 | Parse command line options.
par_download | Function to download multiple file at the same time.
print_help | Printing an usage message from an OptionParser object
rbin | Function to generate executable files for R package
set_colors | Function to get a series defined theme colors
set_tools | Function to generate tools path object
show_handlers | Function to show all avaliabe handler function
show_mhandlers | Function to show all avaliabe mhandler function
split_col_data | Data split function by colum
split_list | Function to split list
split_row_data | Data split function by row
split_row_file | Function to split big file to a series small files (by row)
supress_any_message | suppressWarnings(suppressMessages(...))
time_stamp | Function to generate time stamp in the files name or directories name.