Find Marker Genes At Once¶

findMarkers_one_vs_all()

Identify marker genes for all clusters in a one vs all manner.

findMarkers_one_vs_all(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    cluster_column,
    subset_clusters = NULL,
    method = c("scran", "gini", "mast"),
    pval = 0.01,
    logFC = 0.5,
    min_genes = 10,
    min_expr_gini_score = 0.5,
    min_det_gini_score = 0.5,
    detection_threshold = 0,
    rank_score = 1,
    adjust_columns = NULL,
    verbose = TRUE,
    ...
)

Arguments¶

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
subset_clusters	selection of clusters to compare
method	method to use to detect differentially expressed genes
pval	scran & mast: filter on minimal p-value
logFC	scan & mast: filter on logFC
min_genes	minimum genes to keep per cluster, overrides pval and logFC
min_expr_gini_score	gini: filter on minimum gini coefficient for expression
min_det_gini_score	gini: filter minimum gini coefficient for detection
detection_threshold	gini: detection threshold for gene expression
rank_score	gini: rank scores to include
adjust_columns	mast: column in pDataDT to adjust for (e.g. detection rate)
verbose	be verbose
…	additional parameters for the findMarkers function in scran or zlm function in MAST

Value¶

A data.table with marker genes

Details¶

Wrapper for all one vs all functions to detect marker genes for clusters.