Package index • arcMS

All functions

analysis_search(): Retrieve Analyses from UNIFI API

arcMS arcMS-package: UNIFI MS converter to Parquet and HDF5 formats

collect_one_sample_data(): Collect data from one sample

connection_apihosturl(<connection_params>) connection_token(<connection_params>) connection_identityurl(<connection_params>) connection_username(<connection_params>) connection_password(<connection_params>): Class containing UNIFI API connection parameters

convert_all_samples_data(): Convert data from all samples in an Analysis

convert_bin_to_ccs(): Convert bin value to CCS (Collision Cross Section) value

convert_mzml_to_parquet(): Convert mzML (or mzXML) file to parquet file

convert_one_sample_data(): Convert one sample

create_connection_params(): Create connection parameters

create_sample_dataset(): Create a sample dataset from a Parquet file created by arcMS

folders_search(): Retrieve Folders from UNIFI API

get_connection_params(): Retrieve the connection parameters object

get_sample_infos(): Retrieve Sample Information from UNIFI API with a sample id

get_samples_list(): Retrieve the list of Samples Results from an Analysis in UNIFI API

get_unifi_api_token(): Retrieve the API token in the environment variable

mzml_to_dt(): Convert mzML (or mzXML) file to data.table in long format

mzml_to_sample_dataset(): Convert mzML (or mzXML) file to sample_dataset

run_app(): Run Shiny application to use the conversion package

get_sample_data(<sample_dataset>): Class containing a sample data and metadata

get_sample_metadata(<sample_infos>) get_sample_name(<sample_infos>) get_sample_id(<sample_infos>) get_analysis_name(<sample_infos>) get_sample_metadata_json(<sample_infos>) get_spectrum_metadata(<sample_infos>) get_spectrum_metadata_json(<sample_infos>) add_sample_id(<sample_infos>): Class containing a sample's information

save_one_sample_data(): Save collected data from one sample

send_request(): Check if the connection is still active before current request then return request

store_unifi_api_token(): Save the API token in the .Renviron file for repeated use