FitAsympMarks.UpOrDown: Fit exponential

In jakeyeung/scChIX: Deconvolving Multiplexed Histone Modifications in Single Cells.

Fit exponential

Description

Fit exponential

Usage

FitAsympMarks.UpOrDown(
  dat.exprs.long.gene.lst,
  jmark1 = "H3K4me1",
  jmark2 = "H3K36me3",
  asymp.init = "auto",
  loggamma.init = 0,
  jiter = 1000,
  MaxOrMin = max
)

Arguments

dat.exprs.long.gene.lst	Wrangled data frame for a gene with colnames signal and ptime.exp.norm ready for fitting exponentials across pseudotime
jmark1	name of mark1. In paper it is H3K4me1
jmark2	name of mark2. In paper it is H3K36me3
asymp.init	init asymptote value. "auto" takes MaxOrMin function of the signal. MaxOrMin is "max" or "min". Set "max" if gene is downregulated, set "min" if upregulated.
loggamma.init	init value for log of gamma (time constant)
jiter	number of iterations for fitting nonlinear model
MaxOrMin	"max" or "min". Set "max" if gene is downregulated, set "min" if upregulated.

Value

data.frame of exponential fit outputs on mark1 and mark2

Examples

upordown <- IsUpOrDown(dat.impute.lst, refmark = jmark2, jgene = jgene, dat.meta.long = dat.meta.long)
offset.fn <- ifelse(upordown == "up", min, max)
asymp.init.fn <- ifelse(upordown == "up", max, min)
dat.exprs.long.gene.lst <- SetupDatForGene.UpOrDown(dat.impute.lst, dat.meta.long, jgene, jmark1 = jmark1, jmark2 = jmark2, returnlst = TRUE, offset.zero = TRUE, MaxOrMin = offset.fn)
dat.out <- FitAsympMarks.UpOrDown(dat.exprs.long.gene.lst, jmark1 = jmark1, jmark2 = jmark2, asymp.init = "auto", loggamma.init = 0, MaxOrMin = asymp.init.fn)
outlst <- list(dat.out = dat.out, dat.exprs.long.gene.lst = dat.exprs.long.gene.lst, upordown = upordown)

jakeyeung/scChIX documentation built on May 7, 2023, 9:14 a.m.