runDEAnalysis: Differential expression analysis

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description

Performs differential expression analysis based on previously estimated null and alternative models. (I) Compute loglikelihood of data under null H0 and alternative H1 model. (II) Differential expression analysis as loglikelihood ratio test.

Usage

runDEAnalysis(objLP)

Arguments

objLP

(LineagePulseObject) LineagePulseObject with fitted null and alternative models.

Value

objLP (LineagePulseObject) LineagePulseObject with analysis summary table (dfResults) added.

• Gene: Gene ID.

• p: P-value for differential expression with ZINB noise.

• mean: Inferred mean parameter of constant model of first batch.

• padj: Benjamini-Hochberg false-discovery rate corrected p-value for differential expression analysis with NB noise.

• p_nb: P-value for differential expression with ZINB noise.

• padj_nb: Benjamini-Hochberg false-discovery rate corrected p-value for differential expression analysis with NB noise.

• loglik_full_zinb: Loglikelihood of full model with ZINB noise.

• loglik_red_zinb: Loglikelihood of reduced model with ZINB noise.

• loglik_full_nb: Loglikelihood of full model with NB noise.

• loglik_red_nb: Loglikelihood of reduced model with NB noise.

• df_full: Degrees of freedom of full model.

• df_red: Degrees of freedom of reduced model

• allZero (bool) Whether there were no observed non-zero observations of this gene. If TRUE, fitting and DE analsysis were skipped and entry is NA.

Author(s)

David Sebastian Fischer

See Also

Called by runLineagePulse.

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.