reestimate.pseudos.byCV: reestimate.pseudos.byCV

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

It estimates a new pseudotime for each sample based on its cross-validation estimates.

Usage

reestimate.pseudos.byCV(data, diff.quantile, perc.cutoff,
  pseudotime.cutoff)

Arguments

data	Numeric. A vector of estimated pseudotimes for one sample. The first value corresponds to the estimate of the whole data. The second value is the difference between the estimate of the original data and the median of the CV-estimated pseudotimes and it is used as a dissimilarity measure. The rest of the values are the CV estimated pseudotimes themselves.
diff.quantile	Float. The qth quantile of the distribution of the difference between the original and the CV-estimated pseudotimes. The q parameter is defined in Fluo_CV_modeling().
perc.cutoff	Float. The percentage of CV-estimated pseudotimes that are similar (clustered together by k-means)
pseudotime.cutoff	Integer. A user-defined value to define outlier samples, i.e. samples with Pseudotime(original) - medianPseudotime(CV) > pseudotime.cutoff.

Value

It summarizes the CV-estimated pseudotimes into a single value. There are three possible methods that may produce different results. For details see parameter pseudo.est.method at Fluo_CV().

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.