View source: R/ResultFlagsDependent.R
TADA_FindQCActivities | R Documentation |
This function checks for and flags or removes samples denoted as quality control activities based on the 'ActivityTypeCode' column. The function will flag duplicate samples as "QC_duplicate", blank samples as "QC_blank", calibration or spiked samples as "QC_calibration", and other QC samples as "QC_other". All other samples are flagged as "Non_QC".
TADA_FindQCActivities(.data, clean = FALSE, flaggedonly = FALSE)
.data |
TADA dataframe which must include the column 'ActivityTypeCode' |
clean |
Character argument with options "none", "all", "duplicates", or "blanks", "calibrations", or "other". The default is clean = "none" which does not remove any rows of data. When clean = "all", any rows of data flagged as a Quality Control sample will be removed. When clean = "duplicates", any rows of data flagged as a duplicate Quality Control sample will be removed. When clean = "blanks", any rows of data flagged as a blank Quality Control sample will be removed. When clean = "calibrations", any rows of data flagged as a calibration check or spiked Quality Control sample will be removed. And when clean = "other", any rows of data flagged as some other type of Quality Control sample will be removed. |
flaggedonly |
Boolean argument; the default is flaggedonly = FALSE. When flaggedonly = TRUE, the function will filter the dataframe to show only the rows of data flagged as Quality Control samples. |
This function adds the column "TADA.ActivityType.Flag" to the dataframe which flags quality control samples based on the "ActivityTypeCode" column. When clean = "none", all flagged data are kept in the dataframe. When clean = "all", all flagged data are removed from the dataframe. When clean = "duplicates", data flagged as QC duplicates are removed from the dataframe. When clean = "blanks", data flagged as QC blanks are removed from the dataframe. When clean = "calibrations", data flagged as QC calibration checks or spikes are removed from the dataframe. When clean = "other", data flagged as other QC samples are removed from the dataframe. When flaggedonly = TRUE, the dataframe is filtered to show only the flagged data. When flaggedonly = FALSE, the full, cleaned dataframe is returned. The default is clean = "none" and flaggedonly = FALSE.
# Load example dataset:
data(Data_Nutrients_UT)
# Flag and keep all QC samples:
QC_flagged <- TADA_FindQCActivities(Data_Nutrients_UT)
# Flag QC samples and filter to flagged data only:
QC_flags_only <- TADA_FindQCActivities(Data_Nutrients_UT, flaggedonly = TRUE)
# Remove all QC samples:
QC_clean <- TADA_FindQCActivities(Data_Nutrients_UT, clean = TRUE)
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