getDiffGenes: Detecting lineage dependent differentially expressed genes

In minzheguo/SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy

Detecting lineage dependent differentially expressed genes

Description

given the lineage dependent expression profiles extracted by the getProfiles function, this function first smoothes the expression profile of each gene using cubic regression splines, fits to two models (M1: changes in the lineage; M0: no change), and then uses likelihood ratio test to compare the goodness of fit of the two models and assigns a p-value to each gene

Usage

getDiffGenes(
  profiles,
  diff.thresh = 0.1,
  log.base = 2,
  thresh.exp = 1,
  thresh.cell = 2,
  thresh.var = 0.5
)

Arguments

profiles	The lineage dependent gene expression profiles
diff.thresh	The FDR threshold for significance
thresh.exp	The expression threshold
thresh.cell	The cell number threshold
thresh.var	The variance threshold

Details

Genes meet the following criteria will be selected for likelihood ratio test: expression >=thresh.exp in at least thresh.cell cells and variance>=thresh.var Genes with FDR<diff.thresh will be considered significant

Value

lineage dependent differentially expressed genes and their associated information, e.g., variance, pvalue, fdr, and M1 predicted expression

minzheguo/SLICE documentation built on June 5, 2023, 11:56 a.m.