GEX_phenotype

Adds a column to a VGM[[2]] Seurat object containing cell phenotype assignments. Defaults for T and B cells are available. Marker sets are customizable as below

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Alexander Yermanos

Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis

Andreas Agrafiotis

Victor Kreiner

Tudor-Stefan Cotet

Raphael Kuhn

Danielle Shlesinger

Jiami Han

Vittoria Martinolli D'Arcy

Lucas Stalder

Daphne van Ginneken

GEX_phenotype function

<dl><dt>seurat.object</dt>
<dd>A single seurat object / VDJ_GEX_matrix.output[[2]] object</dd>
<dt>cell.state.names</dt>
<dd>Character vector containing the cell state labels defined by the markers in cell.state.markers parameter. Example is c("NaiveCd4","MemoryCd4").</dd>
<dt>cell.state.markers</dt>
<dd>Character vector containing the gene names for each state. ; is used to use multiple markers within a single gene state. Different vector elements correspond to different states. Order must match cell.state.names containing the c("CD4+;CD44-","CD4+;IL7R+;CD44+").</dd>
<dt>default</dt>
<dd>Default is TRUE - will use predefined gene sets and cell states.</dd></dl>

Arguments

Assignment of cells to phenotypes based on selected markers — GEX_phenotype

<dl>

<dt>seurat.object</dt>
<dd>A single seurat object / VDJ_GEX_matrix.output[[2]] object</dd>


<dt>cell.state.names</dt>
<dd>Character vector containing the cell state labels defined by the markers in cell.state.markers parameter. Example is c("NaiveCd4","MemoryCd4").</dd>


<dt>cell.state.markers</dt>
<dd>Character vector containing the gene names for each state. ; is used to use multiple markers within a single gene state. Different vector elements correspond to different states. Order must match cell.state.names containing the c("CD4+;CD44-","CD4+;IL7R+;CD44+").</dd>


<dt>default</dt>
<dd>Default is TRUE - will use predefined gene sets and cell states.</dd>

</dl>

Assignment of cells to phenotypes based on selected markers

GEX_phenotype: Assignment of cells to phenotypes based on selected markers

Description

Usage

Value

Arguments

Examples