deg.pw: Data frame for example pairwise DEG test result

In rliger: Linked Inference of Genomic Experimental Relationships

Data frame for example pairwise DEG test result

Description

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

defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
degTest <- runPairwiseDEG(
    pbmc,
    groupTest = "stim",
    groupCtrl = "ctrl",
    variable1 = "dataset",
    splitBy = "defaultCluster"
)`

The result is for the DEG test split for each cluster in the dataset, and within each cluster, compare the cells from "stim" against the cells from "ctrl".

Usage

deg.pw

Format

data.frame object of 1743 rows with columns:

• feature: gene names, 249 unique genes repeated 7 times for the tests done for 7 clusters. (1 less cluster than in deg.marker due to too tiny sample size in the smallest cluster)

• group: cluster names, 7 unique cluster names, dividing the tests.

• logFC: log fold change of the gene expression between the condition of interest against the control condition.

• pval: p-value of the DEG test.

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

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

• pct_out: percentage of cells in the control condition expressing the gene.

See Also

runPairwiseDEG()

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