Man pages for rmsharp/snprcspf
SNPRC SPF Colony Screening Data Software Tool Package

add_id_date_repeatedReturns a dataframe with the Id, Date, and Repeated column...
add_sqlmed_codesReturns df dataframe with the SqlMed procedure_name,...
apply_divisorReturns mfi_df with each value divided by the appropriate...
combine_linesReturns character vector of length 1 made up of text found in...
create_luminex_screen_results_tblReturns TRUE if the creation of the pdl_result table was...
create_pdl_results_tblReturns TRUE if the creation of the pdl_results table was...
create_spf_samples_tblReturns TRUE if the creation of the spf_samples table was...
divisors_matchReturns a logical value indicating whether or not the list of...
fix_pdl_csv_columnsReturns pdl_df with columns renamed, added and ordered to...
format_luminex_resultsReturns Excel file name of file that has been formatted to...
get_agents_and_antigen_pairsReturns dataframe of possible antigen pairs and agents
get_all_combinedReturns dataframe with multiple combined results from antigen...
get_all_dfReturns a dataframe with all bead or all summary results...
get_all_filesReturns the list of pathology report files with an extension...
get_all_regionsReturns a dataframe with the files, order, and Region[@name]s...
get_all_summary_dfReturns a dataframe with all summary results combined.
get_antigen_pairsReturns a dataframe with the agent and two antigens used to...
get_assay_pairsReturns a dataframe, with sets of assays with an antibody...
get_bad_date_ids_and_id_idsReturns a list with two character vectors containing the...
get_bead_dfGet bead call multipliers from results section of Excel SPF...
get_bead_headersReturns a dataframe with all headers found in the bead...
get_col_boundariesReturns an integer vector with the the positions in the line...
get_col_namesReturns character vector of column names base on type...
get_combinedReturns dataframe with combined results from antigen results
get_date_from_sampleReturns the date from a sample column if it exist else NA.
get_divisor_mismatchReturns a charcter vector with the file names of files that...
get_divisorsReturns a named numeric vector with the divisors originally...
get_empty_pdl_dfReturns empty pdl_df
get_excel_divisorsReturns a named numeric vector with the divisors originally...
get_file_idsReturns integer vector with plate numbers
get_followupReturns "followup" assay results, which are groups of assay...
get_followup_pool_samplesReturns assay results for individual animals based on assay...
get_id_date_repeatedReturns dataframe with true animal Ids (Id) and date strings...
get_id_from_sampleReturns the first integer value from a sample column if it...
get_low_positive_controlsFinds any wells with low positive controls
get_luminex_speciesReturns species desination of "CYNO", "MACAQUE" or "PAPIO" at...
get_Machine_infoReturns Machine serialNumber, name, sftwareVersion,...
get_mean_raw_mfiReturns dataframe with means of replicated samples
get_mean_raw_mfi_from_lxdReturns the mean_raw_mfi_df from an XML file (.lxd extension)...
get_mean_raw_mfi_from_xlsxReturns the mean_raw_mfi_df from an Excel file (.xlsx...
get_melted_bead_2_wideReturns bead based wide dataframe from bead based melted...
get_most_recent_fileReturns the most recent assay file name for each plate number
get_most_recent_filesReturns the most recent assay file name for each plate number
get_one_record_dfReturns a one record dataframe with the data from one assay...
get_pdl_csv_dataReturns pdl data from their CSV files given a list of...
get_pdl_meta_data_from_contentReturns specified value from a pdl_report$content object
get_pdl_nonnegative_reportsReturns non-negative results from PDL reports results
get_pdl_report_dateReturns report date from a pdl_report object
get_pdl_report_file_nameReturns report file name from a pdl_report object
get_pdl_reportsReturns a list of lists of length two containing $content and...
get_pdl_resultsGet PDL results
get_pdl_results_test_commentReturns a character vector of length 2 with the result and...
get_plateIDReturns Plate[@plateID] (plateID attribute of the Plate...
get_pooled_sample_dfReturns dataframe with animal Ids, cage location, bleed date,...
get_positive_antigensReturns positive antigens based on low control value and a...
get_possible_ids_datesReturns a list of length 2 with possible$ids and...
get_raw_mfiReturns dataframe of original values
get_raw_mfi_dfReturns dataframe with raw mfi values from the raw section of...
get_raw_mfi_tablesReturns character vector with the raw data (raw mfi) table
get_region_dfReturns a dataframe with region order, region name, and...
get_repeated_from_sampleReturns a character vector of 'Y' if the sample indicates it...
get_report_date_from_filenameReturns report date in yyyy-mm-dd format as derived from the...
get_result_tablesReturns character vector with the result tables
getRunPropertyValueReturns value of run property if one is available else NA is...
get_sample_dfReturns dataframe with animal Ids, cage location, bleed date,...
get_sample_type_transReturns the corrected sample type given slightly malformed or...
get_session_date_tmReturns date and time of assay based on '//Plate[@name].
get_setup_nameReturns the Setup[@name]s for a lum
get_snprc_idReturns an SNPRC animal Id of the pdl_animal_id represents an...
get_start_end_datesReturns data frame with file and start_date as the two...
get_still_posGet dataframe of animals where the most recent assay was not...
get_summary_dfReturns dataframe with summary results from the results...
get_test_antigens#' Makes function to return agents and antigen pairs. #' #'...
getTransformedOutputFileReturns full name with path of transformed output file.
get_usable_filesReturns a character vector of names of usable files.
get_wide_dfReturns a list of dataframes that have been converted to wide...
get_workset_descReturns /WorkSet/Description from XML
get_yyyymmdd_from_possible_datesReturns yyyymmdd in with optional separator between date...
handleErrorsAndWarningsReturns NULL: does not return - writes the maximumSeverity...
insert_combined_assay_resultsReturns the number of saved records
insert_missing_linesReturns character vector representing the contents of the...
insert_pdl_resultsReturns the number of records inserted into pdl_results
insert_spf_samplesReturns the number of records inserted into spf_samples
is_column_labelsReturns TRUE if a line is an expected set of column labels
luminex_agent_to_sqlmed_test_idReturns a numeric vector of SqlMed test_id given a character...
luminex_agent_to_sqlmed_test_nameReturns a character vector of SqlMed test_name given a...
luminex_to_sqlmed_procedure_idReturns a numeric vector of SqlMed procedure_id given a...
luminex_to_sqlmed_procedure_nameReturns a character vector of SqlMed procedure_names given a...
make_excel_wkbkForm an Excel workbook and worksheet similar in format to...
mdy_to_yyyymmddReturns character vector of dates where entities of mm/dd/yy...
merge_pooled_and_pdlReturns a dataframe with pooled_df merged with pdl_df by...
na_to_charReplaces an NA value with a character string
pdl_assay_to_sqlmed_procedure_idReturns a character vector of SqlMed procedure_id given a...
pdl_assay_to_sqlmed_procedure_nameReturns a character vector of SqlMed procedure_names given a...
pdl_assay_to_sqlmed_test_idReturns a character vector of SqlMed test_id given a...
pdl_assay_to_sqlmed_test_nameReturns a character vector of SqlMed test_name given a...
pdl_reports_to_dfReturns dataframe with results from all report files in...
pdl_report_to_dfReturns dataframe with parsed content of pdl_report
pooled_bleed_date_to_sample_dateReturns pooled_df dataframe with bleed_date replaced by...
pooled_Y_or_NReturns "Y" if a sample is pooled and "N" if it is an...
print_bad_animal_idsReturns a dataframe of file names, sample, snprc_id, and...
print_bad_sample_datesReturns a dataframe of file names, LocName, animal Id, and...
readRunPropertiesFileReturns a dataframe with four columns ("name", "value",...
read_sample_fileRead blood or dna sample file
remove_bad_animal_idsReturns only good SNPRC animal Ids given a character vector...
remove_bn_and_dash_RReturns samples with "Bn" and "-R" trimmed off of each end
remove_pdl_report_headersReturns content for PDL reports without introductory material...
replace_bad_csv_filesReturns a dataframe with a row for each bad CSV file with the...
report_missing_samplesCreates an Excel file with a list of samples that were...
report_unexpected_samplesReturns a list of samples that were expected but not...
save_excel_sheetReturns the file name of the Excel file created which...
setMaxSeverityReturns integer value of error level (0:NONE, 1:WARN,...
sort_occurancesReturns a sorted dataframe with First occurrances appearing...
spf_odbcConnectReturns database connection object
strip_column_labelsReturns content minus column labels. Fails with a call to...
subtract_backgroundReturns mfi_df dataframe values with wBAC column subtracted...
test_for_bleed_dateThrows and error on one or more provided bleed dates occur on...
test_for_cageThrows and error on one or more bad cage numbers are...
test_for_snprc_idThrows and error on one or more bad animal Ids. It terminates...
test_for_yes_noThrows and error on bad input for the 'expected_blood' or...
triggerErrorReturns NULL: does not return - triggers error and stops...
triggerWarningReturns 'run_error', after setting 'run_error$level' to 1 if...
rmsharp/snprcspf documentation built on Nov. 18, 2017, 8:19 p.m.