Identify Marker Genes in a One vs All Manner

findScranMarkers_one_vs_all()

Identify marker genes for all clusters in a one vs all manner based on scran’s implementation of `findMarkers <findMarkers>`_.

findScranMarkers_one_vs_all(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    cluster_column,
    subset_clusters = NULL,
    pval = 0.01,
    logFC = 0.5,
    min_genes = 10,
    verbose = TRUE,
    ...
)

Arguments

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
subset_clusters	subset of clusters to use
pval	filter on minimal p-value
logFC	filter on logFC
min_genes	minimum genes to keep per cluster, overrides pval and logFC
verbose	be verbose
…	additional parameters for the findMarkers function in scran

Value

A data.table with marker genes.

..seealso::

findScranMarkers.

Examples

Note

When ‘Scran’ to detect marker genes. If used in published research, please cite: Lun, A. T., McCarthy, D. J., & Marioni, J. C. (2016). A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Research, 5.

data(mini_giotto_single_cell)

scran_markers = findScranMarkers_one_vs_all(gobject = mini_giotto_single_cell,

cluster_column = ‘leiden_clus’)

#> F1000Res., 5, 2122. doi: 10.12688/f1000research.9501.2. #> #> start with cluster 1 #> #> start with cluster 2 #> #> start with cluster 3