summarize quality control for clustering and for quality control sample variation based on compound ($SpecAbund) and feature ($MSdata and $MSMSdata, if present)
rc.remove.qc(ramclustObj = NULL, qc.tag = "QC")new RC object. moves QC samples to new $qc slot from original position.
ramclustR object to analyze
qc.tag character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot (i.e. c("QC", "sample.type"). If length one (i.e. "QC"), will search for this string in the 'sample.names' slot by default.
Corey Broeckling
simply moves QC samples out of the way for downstream processing. moved to a $qc slot.
Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.
Broeckling CD, Ganna A, Layer M, Brown K, Sutton B, Ingelsson E, Peers G, Prenni JE. Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction. Anal Chem. 2016 Sep 20;88(18):9226-34. doi: 10.1021/acs.analchem.6b02479. Epub 2016 Sep 8. PubMed PMID: 7560453.