Next-Generation Sequencing (NGS) Data Analysis Toolkit


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Documentation for package ‘ngstk’ version 0.2.3

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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.