vgam_deg: vgam_deg identifies genes that were differentially expressed...

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

vgam_deg identifies genes that were differentially expressed along the re-ordered single-cell trajectories using vgam

Usage

vgam_deg(exprs = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup.txt", order,
  lm_order = c("CD115+CDP_2", "CD115+CDP_1", "PreDC_9", "PreDC_3"),
  min_expr = 1, p_threshold = 0.05)

Arguments

exprs	a data frame or matrix of expression data(ie. rpkm, TPM, fpkm) or a tab delimited txt file of expression data, containing cells in columns and genes in rows
order	a vector of re-ordered cell IDs
lm_order	a vector of landmark IDs indicating along which path the cells are to be sorted
min_expr	a numeric value indicating the minimum TPM value for a gene to be considered as expressed. Default is 1.
p_threshold	p value cutoff for selecting differentially expressed genes.

Value

deg: a list of differentially expressed genes

Examples

## Not run: 
deg <- vgam_deg(exprs = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup.txt",
                order = order,
                lm_order = c("CDP_2","CDP_1","preDC_9","preDC_3"),
                min_expr=1,
                p_threshold=0.05)

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.