deg.marker: Data frame for example marker DEG test result

In rliger: Linked Inference of Genomic Experimental Relationships

Data frame for example marker DEG test result

Description

The data frame is the direct output of marker detection DEG test applied on example dataset which can be loaded with data("pbmc"). The DEG test was done with:

defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
deg.marker <- runMarkerDEG(
    pbmc,
    minCellPerRep = 5
)

The result is for the marker detection test for 8 clusters in the dataset by comparing each cluster against all other clusters.

Usage

deg.marker

Format

data.frame object of 1992 rows with columns:

• feature: gene names, 249 unique genes repeated 8 times for the tests done for 8 clusters.

• group: cluster names, 8 unique cluster names, dividing the tests.

• logFC: log fold change of the gene expression between the cluster of interest against all other clusters.

• pval: p-value of the DEG test.

• padj: adjusted p-value of the DEG test.

• pct_in: percentage of cells in the cluster of interest expressing the gene.

• pct_out: percentage of cells in all other clusters expressing the gene.

See Also

runMarkerDEG()

rliger documentation built on Oct. 30, 2024, 1:07 a.m.