Can parameters obtained from IPO's grouping optimization be used in both the alignment and grouping steps using PeakGroupsParam during alignment?

[YUANMENG-1]

Can the parameters optimized by IPO for peak grouping be used for both the alignment and grouping steps? I don't want to use the IPO-optimized orbiwarp results, but it seems IPO states that it can only optimize the orbiwarp method for alignment: "The method getDefaultRetGroupStartingParams only supports one retention time correction method (obiwarp) and one grouping method (density) at the moment.

Like this:?

Set initial density parameters

pdp <- PeakDensityParam(sampleGroups = pheno$Group, bw = 10,
minFraction = 0.772, binSize = 0.01)

First grouping

mse <- groupChromPeaks(data, pdp)

Adjust retention time using peak groups parameters

pgm <- adjustRtimePeakGroups(mse, PeakGroupsParam(minFraction = 0.772))

Adjust retention time parameters

pgp <- PeakGroupsParam(minFraction = 0.772, span = 0.6)
mse <- adjustRtime(mse, param = pgp)

Second grouping using the same density parameters

mse2 <- groupChromPeaks(mse, pdp)

The parameters bw = 10, minFraction = 0.772, binSize were obtained from IPO's grouping optimization. Can these parameters be used in both the alignment and grouping steps like this?

[YUANMENG-1]

I see here: The XCMS-methods supported by IPO for retention time correction include loess

But https://bioconductor.org/packages/release/bioc/vignettes/IPO/inst/doc/IPO.html said: The method getDefaultRetGroupStartingParams only supports one retention time correction method (obiwarp) and one grouping method (density) at the moment.

[rietho]

Hi @YUANMENG-1 , IPO is currently in the unsupported state, which means that it is not actively maintained. I was maintaining the package some years ago, but can't remember enough to answer your question.

An approach to get an answer might be to look at the source code yourself. Or maybe someone from the community can help.