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?