annotateCellTypesGSEA: Match deconvolved cell-types to ground truth cell-types based...

In JEFworks-Lab/STdeconvolve: Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Match deconvolved cell-types to ground truth cell-types based on transcriptional profiles

Description

Match deconvolved cell-types to ground truth cell-types by testing for enrichment of ground truth marker gene sets in the deconvolved transcriptional profiles. Uses fgsea Korotkevich G, Sukhov V, Sergushichev A (2019). “Fast gene set enrichment analysis.” bioRxiv. doi:10.1101/060012, http://biorxiv.org/content/early/2016/06/20/060012.

Usage

annotateCellTypesGSEA(beta, gset, qval = 0.05, ...)

Arguments

beta	cell-type (rows) x gene (columns) matrix of deconvolved cell-type transcriptional profiles
gset	named list where each entry is a vector of marker genes for a given ground truth cell-type.
qval	adjusted p-value threshold (default: 0.05)
...	additional options for fgsea

Value

A list that contains

• results: A named list that contains sorted matrices for each deconvolved cell-type. The matrix rows are the ground truth cell-types ordered by significance, edge-score, and enrichment score of their gene sets in the deconvolved transcriptional profile of a given deconvolved cell-type.

• predictions: a named vector where the names are the deconvolved cell-types and the values are the best matched ground truth cell-type that is also positively enriched.

JEFworks-Lab/STdeconvolve documentation built on Nov. 14, 2024, 7:24 p.m.