FitMixingWeightPtimeLinear.fixedw: Infer pseudotime1 and pseudotime2 from a double-incubated...

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

Infer pseudotime1 and pseudotime2 from a double-incubated cell

Description

Infer pseudotime1 and pseudotime2 from a double-incubated cell

Usage

FitMixingWeightPtimeLinear.fixedw(
  cell.count.raw.merged,
  jfits.lowess1,
  jfits.lowess2,
  w.fixed,
  p1.init,
  p1.lower,
  p1.upper,
  p2.init,
  p2.lower,
  p2.upper,
  jmethod = "L-BFGS-B",
  jhessian = FALSE
)

Arguments

cell.count.raw.merged	vector of raw cell counts from a double-incubated cell. If KNN smoothing, then this vector is the sum of the double-incubated cell and its nearest K neighbors (K=25 used in paper).
jfits.lowess1	Named list of "smooth.spline" outputs (lowess fits) for mark1. Each element in list is accessible by a gene name that matches the names in cell.count.raw.merged
jfits.lowess2	Named list of "smooth.spline" outputs (lowess fits) mark2. Each element in list is accessible by a gene name that matches the names in cell.count.raw.merged
w.fixed	Fixed weighting between mark1 and mark2. In paper we used w=0.77, optimized by running scChIX for different w's. Fixing w for all cells makes for more stable outputs than a cell-specific w
p1.init	init pseudotime1 [0, 1]
p1.lower	lowerbound for pseudotime1 (eg 0)
p1.upper	upperbound for pseudotime1 (eg 1)
p2.init	init pseudotime2 [0, 1]
p2.lower	lowerbound for pseudotime2 (eg 0)
p2.upper	upperbound for pseudotime2 (eg 1)
jmethod	method for optimizing: use one that allows constraints like "L-BFGS-B"
jhessian	return hessian (TRUE or FALSE). TRUE allows one to estimate the standard errors of the pseudotime estimates afterwards.

Value

optim output for best pseudotime1 and pseudotime2 that fits the double-incubated cell

Examples

jfits.lst <- parallel::mclapply(jcells, function(jcell){
  cell.count.raw.merged <- mat.dbl[, jcell]
  jfit.fixedw <- FitMixingWeightPtimeLinear.fixedw(cell.count.raw.merged = cell.count.raw.merged, jfits.lowess1 = fits.lowess1.linear, jfits.lowess2 = fits.lowess2.linear, w.fixed = w.fixed, p1.init = 0.5, p1.lower = 0.01, p1.upper = 0.99,  p2.init = 0.5, p2.lower = 0.01, p2.upper = 0.99, jmethod = "L-BFGS-B", jhessian = TRUE)
}, mc.cores = ncores)

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