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
annotateCellTypesGSEA R Documentation
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 liger::iterative.bulk.gsea.
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)
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 April 14, 2023, 1:04 p.m.
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| annotateCellTypesGSEA | R Documentation |
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 liger::iterative.bulk.gsea.
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) |
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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