SetupDatForGene.UpOrDown: Check if gene is up- or down-regulated

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

Check if gene is up- or down-regulated

Description

Check if gene is up- or down-regulated

Usage

SetupDatForGene.UpOrDown(
  dat.impute.lst,
  dat.meta.long,
  jgene,
  jmark1 = "H3K4me1",
  jmark2 = "H3K36me3",
  refmark = "H3K36me3",
  returnlst = TRUE,
  offset.zero = TRUE,
  frac.cells.filter = 0.01,
  MaxOrMin = max
)

Arguments

dat.impute.lst	list of matrices (rows are genes, columns are cells). Each matrix is a different histone mark
dat.meta.long	data frame of metadata for individual cells. Column names include cell, mark, and ptime.expnorm (pseudotime)
jgene	name of gene (row name) found in the matrix
jmark1	name of mark1. In paper it is H3K4me1
jmark2	name of mark2. In paper it is H3K36me3
refmark	name of refmark. In paper it is H3K36me3
returnlst	return list split by mark
offset.zero	set min(signal) to be zero if upregulated, set max(signal) to be zero if downregulated
frac.cells.filter	deprecated input, ignore it
MaxOrMin	"max" or "min". Set "max" if gene is downregulated, set "min" if upregulated.

Value

dat.exprs.long.annot: Wrangled data frame for a gene, annotated with pseudotime across cells and marks. Ready for fitting exponentials.

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)

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