Get Parameters for QC-RLSC Normalization

Obtain parameters for quality control-based robust LOESS (locally estimated scatterplot smoothing) signal correction

Usage

get_params(
  omicsData,
  block_cname,
  qc_cname,
  qc_ind,
  order_cname,
  missing_thresh,
  rsd_thresh
)

Arguments

omicsData

an omicsData object (metabData, lipidData, pepData, or proData) created using the pmartR package, where any zero values have already been replaced with NAs and a log transformation has already been applied

block_cname

character string giving name of column in omicsData$f_Data that contains block (or batch) information

qc_cname

character string giving name of column in omicsData$f_data that contains the factor variable indicating whether sample is QC or not

qc_ind

character string giving the value from the qc_cname column that indicates a QC sample

order_cname

character string giving name of column in omicsData$f_data that contains the run order

missing_thresh

numeric threshold, between 0 and 1, used for filtering out biomolecules. See details for more information. A value of 0.5 is reasonable.

rsd_thresh

numeric threshold used for filtering metabolites. See details for more information. A value of 0.3 is reasonable.

Value

list with elements final_ests (used as optimal_params input argument to qcrlsc) and bad_feats (features, or biomolecules, that need to be filtered out prior to using qcrlsc)

Details

Use this function to get the optimal parameter values to use in a subsequent call to qcrlsc, as well as a list of biomolecules that should be removed from the dataset prior to QC-RLSC normalization

References

Dunn,W.B., Broadhurst,D., Begley,P., Zelena,E., Francis-McIntyre,S., Anderson,N., Brown,M., Knowles,J.D., Halsall,A., Haselden,J.N. et al. (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat. Protoc., 6, 1060-1083

Author

Lisa Bramer, Kelly Stratton