LRcell: Cell-type enrichment analysis for preranked gene set.

In marvinquiet/LRcell: Differential cell type change analysis using Logistic/linear Regression

Cell-type enrichment analysis for preranked gene set.

Description

This function wraps around LRcellCore in case of empty inputs of the marker gene file and brain region.

Usage

LRcell(
  gene.p,
  marker.g = NULL,
  species = c("mouse", "human"),
  region = NULL,
  method = c("LR", "LiR"),
  min.size = 5,
  sig.cutoff = 0.05
)

Arguments

gene.p	Named vector of gene-level pvalues from DEG analysis, i.e. DESeq2, LIMMA
marker.g	List of Cell-type specific marker genes derived from single-cell RNA-seq. The name of the list is cell-type or cluster name, the values are marker genes vectors or numeric named vectors. LRcell provides marker genes list in different human/mouse brains, but users could use their own marker gene list as input. default: NULL
species	Either 'mouse' or 'human', default: mouse.
region	Specific brain regions provided by LRcell. For mouse, LRcell provides 9 brain regions: c("FC", "HC", "PC", "GP", "STR", "TH", "SN", "ENT", "CB"). For human, LRcell provides c("pFC", "PBMC")
method	Either 'logistic regression' or 'linear regression'. Logistic regression equally treats cell-type specific marker genes, however, if certain values could determine the importance of marker genes, linear regression can be performed, default: LR.
min.size	Minimal size of a marker gene set, will impact the balance of labels
sig.cutoff	Cutoff for input genes pvalues, default: 0.05.

Value

A list with LRcell results. Each item represents a marker gene input. Each item in this list is a statistics table. In the table, the row represents the name of marker genes, and the columns are:

• ID The IDs of each marker genes, can be a cell type or cluster;

• genes_num How many marker genes are contributing to the analysis;

• coef The coefficients of Logistic Regression or Linear Regression;

• odds_ratio The odds ratio quantifies association in Logistic Regression;

• p-value The p-value calculated from the analysis;

• FDR The FDR after BH correction.

• lead_genes Genes that are contributing to the analysis;

Examples

data(example_gene_pvals)
res <- LRcell(example_gene_pvals, species="mouse", region="FC", method="LR")

marvinquiet/LRcell documentation built on Sept. 16, 2022, 9:09 a.m.