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

snATAC.RePACT

R Documentation

snATAC.RePACT

Description

This function is to run logistic regression based on the number of LSIs, and characteristics of samples.

Usage

snATAC.RePACT(
  OBJ,
  Sample,
  pheno,
  pheno_levels,
  is_continuous = F,
  if_donorWise = F,
  binnumber = 20,
  LSIrange = "",
  RePACT_qvalCut = 0.01,
  donorWise_qvalCut = 0.01
)

Arguments

`OBJ,`	a snATAC-seq Seurat object, assay name is "peak"
`Sample,`	colnames of donor or sample infomation in OBJ@meta.data
`pheno,`	the column name of the "characteristics to compare" in OBJ@meta.data, e.g. diseaseStatus or BMI or HBA1C
`pheno_levels,`	specify the levels of pheno column. e.g. c("HT", "T2D"), specify for binary pheno
`is_continuous,`	if pheno is continous variable. default is F. e.g. diseaseStatus is F, BMI is T
`if_donorWise,`	if perform donor wise RePACT, default is F
`binnumber,`	number of bins for cell grouping
`RePACT_qvalCut,`	qvalue cutoff to determine the significant genes along the disease or other characteristics trajactory, certain cutoff for slope can be further applied
`donorWise_qvalCut,`	qvalue cutoff to determine the significant genes varying within donors or across donors.
`LSIrange.`	default is "", automatically take top 10 LSIs that are significant with phenotype, otherwise specify 10 LSIs, e.g. 1:10 or 2:11