runTauStarDE: Perform Differential Expression Test by tauStar on a List of...

In SONGDONGYUAN1994/PseudotimeDE: Inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data

Perform Differential Expression Test by tauStar on a List of Genes

Description

Test if each gene in a list of genes is differentially expressed along pseudotime. A wrapper of tauStarDE::tauStarDE.

Usage

runTauStarDE(
  gene.vec,
  ori.tbl,
  mat,
  assay.use = "counts",
  seurat.assay = "RNA",
  mc.cores = 2,
  mc.preschedule = TRUE,
  SIMPLIFY = TRUE
)

Arguments

gene.vec	A vector of genes. It should be a subset of the row names in sce.
ori.tbl	A tibble or dataframe which contains the original cells and pseudotime as two columns.
mat	The input expression data. It can be: (1) A SingleCellExperiment object which contain the expression data; (2) An matrix; (3) A Seurat object which contain the expression data. Its row names should be genes and col names should be cells.
assay.use	The assay used in SingleCellExperiment or slot used in Seurat. Default is counts.
seurat.assay	The assay used in Seurat. Default is 'RNA'.
mc.cores	Number of cores for computing.
mc.preschedule	See mclapply. Default is TRUE.
SIMPLIFY	A logic variable whether to return a tibble (TRUE) or a list of lists (FALSE). Default is TRUE.

Value

A tibble of summary results of genes

Author(s)

Yuheng Lai

Examples

data("LPS_sce")
data("LPS_ori_tbl")
data("LPS_sub_tbl")
res <- PseudotimeDE::runTauStarDE(gene.vec = c("CCL5", "CXCL10"),
ori.tbl = LPS_ori_tbl, sub.tbl = LPS_sub_tbl[1:10], mat = LPS_sce, model = "nb")

SONGDONGYUAN1994/PseudotimeDE documentation built on Jan. 23, 2025, 7:15 a.m.