findScranMarkers_one_vs_all

Source: R/differential_expression.R

Identify marker genes for all clusters in a one vs all manner based on scran's implementation of 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

data.table with marker genes

See also

findScranMarkers

Examples


data(mini_giotto_single_cell)

scran_markers = findScranMarkers_one_vs_all(gobject = mini_giotto_single_cell,
                                            cluster_column = 'leiden_clus')

#> using 'Scran' to detect marker genes. If used in published research, please cite:
#>   Lun ATL, McCarthy DJ, Marioni JC (2016).
#>   'A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.'
#>   F1000Res., 5, 2122. doi: 10.12688/f1000research.9501.2. 
#> 
#>  start with cluster  1 
#> 
#>  start with cluster  2 
#> 
#>  start with cluster  3