CallT2Dpeak_qvalue_SpeedUP: CallT2Dpeak_qvalue_SpeedUP This function is to run regression...

In chenweng1991/RePACT: What the Package Does (One Line, Title Case)

CallT2Dpeak_qvalue_SpeedUP This function is to run regression (linear/logistic) based on the number of PCs, and characteristics of samples.

Description

This function is to call dynamic peaks along the phenotype trajectory

Usage

CallT2Dpeak_qvalue_SpeedUP(
  cellvsPeak.m.aggr = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$cellvsPeak.m.aggr,
  depths = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$depths,
  index = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$index,
  qcut = 0.1,
  slopecut1 = 0.5,
  slopecut2 = -0.5,
  doscale = T
)

CallT2Dpeak_qvalue_SpeedUP(
  cellvsPeak.m.aggr = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$cellvsPeak.m.aggr,
  depths = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$depths,
  index = ATAConCCA.betaT2D.tjct.3nd.10bin.ob$index,
  qcut = 0.1,
  slopecut1 = 0.5,
  slopecut2 = -0.5,
  doscale = T
)

Arguments

cellvsPeak.m.aggr,	a vector of peaks (":" "-")
depths	total fragments of cells within each traj_bin
index	avg pseudo-index of each bin
qcut	qvalue cutoff to measure the significance of glm(expr~index)
slopecut1	UP slope cutoff, slope from glm(expr~index), UP genes
slopecut2	DN slope cutoff, slope from glm(expr~index), DN genes
doscale	if build glm model based on scaled_expression and scaled pseudo-inddex
depths,	RePACT reesult OBJ
index,	RePACT reesult OBJ
qcut,	qvalue cutoff, default qcut=0.1
slopecut1,	slope cutoff for UP-regulated genes/peaks, default slopecut1=0.5
slopecut2,	slope cutoff for DN-regulated genes/peaks,default slopecut2=-0.5
doscale,	if the regression is performed on scaled index and expr data, default doscale=T

Value

The function return a list: "PCvariance", "PCanfpheno", "object.raw.withinfo", "model", "reg.plot.2d", "model.para"

The function return a list of plots, pseudoregress.all contains summary statistics for all genes/peaks,

Examples

betaT2D.diffGene.20bin.PCA <- CallT2Dpeak_qvalue_SpeedUP(beta.RNA.PCA.20bin.ob$cellvsPeak.m.aggr, depths=beta.RNA.PCA.20bin.ob$depths, index=beta.RNA.PCA.20bin.ob$index, qcut=0.2,slopecut1=0.3,slopecut2=-0.3,doscale=T)

chenweng1991/RePACT documentation built on Aug. 28, 2023, 6:28 p.m.