crossweight: Perform crossweighting

In pcahan1/epoch: Dynamic GRN reconstruction from single cell RNA-Seq data

Description

Perform crossweighting

Usage

crossweight(
  grnTab,
  expDat,
  xdyn,
  lag = floor(ncol(expDat)/5),
  min = ceiling(ncol(expDat)/50),
  max = floor(ncol(expDat)/12),
  symmetric_filter = FALSE,
  filter_thresh = 0
)

Arguments

grnTab	GRN dataframe, the result of running reconstructGRN or reconstructGRN_GENIE3
expDat	genes-by-cells expression matrix
xdyn	result of running findDynGenes
lag	lag window on which to run cross-correlation. Cross-correlaiton computed from -lag to +lag.
min	minimum of weighting window. Edges with offsets (or absolute offsets if symmetric_filter=TRUE) less than min will not be negatively weighted.
max	maximum of weighting window. Edges with offsets (or absolute offsets if symmetric_filter=TRUE) greater than max will have weights set to 0.
symmetric_filter	whether or not to employ a symmetric weight scheme. If true, absolute offset is used in place of offset.
filter_thresh	after crossweighting, edges with weights less than filter_thresh will be set to 0.

Value

grnTab with offset and weighted_score added

pcahan1/epoch documentation built on Feb. 14, 2022, 1:57 a.m.