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103 lines (102 loc) · 3.11 KB
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# Generated by roxygen2: do not edit by hand
export(assess_noninferable_proteins)
export(assess_redundant_protein_matches)
export(best_PTM_location_by_ascore)
export(compute_num_peptides_per_1000aa)
export(create_crosstab)
export(create_msnset)
export(filter_masic_data)
export(filter_msgf_data)
export(filter_msgf_data_missed_cleavages)
export(filter_msgf_data_peptide_level)
export(filter_msgf_data_protein_level)
export(get_AScore_results)
export(get_dms_job_records)
export(get_job_records_by_dataset_package)
export(get_output_folder_for_job_and_tool)
export(get_results_for_multiple_jobs)
export(get_results_for_multiple_jobs.dt)
export(get_results_for_single_job)
export(get_results_for_single_job.dt)
export(get_study_design_by_dataset_package)
export(get_tool_output_files_for_job_number)
export(is_PNNL_DMS_connection_successful)
export(make_results_ratio_gl)
export(make_results_ratio_ph)
export(make_rii_peptide_gl)
export(make_rii_peptide_ph)
export(path_to_FASTA_used_by_DMS)
export(read_AScore_results)
export(read_masic_data)
export(read_masic_data_from_DMS)
export(read_msgf_data)
export(read_msms_data_from_DMS)
export(read_study_design)
export(remap_accessions_refseq_to_gene)
export(remap_accessions_refseq_to_gene_fasta)
export(remap_accessions_uniprot_to_gene)
export(remap_accessions_uniprot_to_gene_fasta)
importFrom(AnnotationDbi,select)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,query)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,reduce)
importFrom(MSnID,MSnID)
importFrom(MSnID,MSnIDFilter)
importFrom(MSnID,apply_filter)
importFrom(MSnID,mass_measurement_error)
importFrom(MSnID,optimize_filter)
importFrom(MSnID,psms)
importFrom(MSnbase,MSnSet)
importFrom(MSnbase,pData)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(odbc,dbClearResult)
importFrom(odbc,dbConnect)
importFrom(odbc,dbDisconnect)
importFrom(odbc,dbFetch)
importFrom(odbc,dbSendQuery)
importFrom(odbc,odbc)
importFrom(plyr,llply)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(readr,read_tsv)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(tidyselect,all_of)
importFrom(tidyselect,contains)
importFrom(tidyselect,starts_with)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importMethodsFrom(MSnID,"$<-")
importMethodsFrom(MSnID,"psms<-")
importMethodsFrom(MSnID,accessions)