findMarkers: Find markers in scRNA-seq data

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Find markers in scRNA-seq data

Description

findMarkers Uses Seurat to find markers in scRNA-seq data and returns a table of markers and labels that can be used by CellWalker. This implementation uses default parameters and is designed for a simple first pass for creating labels.

Usage

findMarkers(
  RNAMat,
  genes,
  barcodes,
  dims = 1:10,
  resolution = 0.5,
  only.pos = FALSE
)

Arguments

RNAMat	gene-by-barcode matrix of scRNA data
genes	character vector of gene names
barcodes	character vector of barcodes
dims	integer vector of PCA dimensions to use
resolution	numeric resolution to use in Louvain clustering
only.pos	only return positive markers

Value

table of marker genes, labels, and logFC in expression

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.