QC-RLSC Normalization — normalize

Quality control-based robust LOESS (locally estimated scatterplot smoothing) signal correction

Usage

normalize_qcrlsc(
  omicsData_filt,
  optimal_params,
  block_cname,
  qc_cname,
  qc_ind,
  backtransform = FALSE,
  keep_qc = FALSE
)

Arguments

omicsData_filt: 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, where any biomolecules that were identified by get_params() as needing to be removed have been removed
optimal_params: final_ests element of the output from get_params() function (this is needed for Span and Poly_Degree values)
block_cname: character string giving name of column in omicsData_filt$f_Data that contains block (or batch) information. Values in this column must be numeric.
qc_cname: character string giving name of column in omicsData_filt$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
backtransform: logical value indicated whether or not to backtransform the data to put the normalized data back on the same scale as the original data. Defaults to FALSE. If TRUE, the median of the y-values of the loess curve is added to the normalized value for each biomolecule for each batch.
keep_qc: logical value to determine whether or not to include QC samples in the final output of the data (default is set to FALSE)

Value

omicsData object of same class as omicsData_filt, where e_data contains the QC-RLSC normalized values

Details

This function applies the QC-RLSC normalization to each batch of input data. Must use get_params function first in order to get optimal_params input for qcrlsc.

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

Kelly Stratton, Lisa Bramer