assignCellsByScores: Assign Cells By Scores

In khodosevichlab/CellAnnotatoR: Automated marker-based cell type annotation

Assign Cells By Scores

Description

Assign cell types for each cell based on type scores. Optionally uses 'clusters' to expand annotation.

Usage

assignCellsByScores(
  graph,
  clf.data,
  score.info = NULL,
  clusters = NULL,
  verbose = 0,
  uncertainty.thresholds = c(coverage = 0.5, negative = 0.5, positive = 0.75),
  max.depth = NULL,
  ...
)

Arguments

graph	cell graph from Seurat, Pagoda2 or some other tool. Can be either in igraph or adjacency matrix format. Use 'graph=NULL' to skip graph diffusion step and get raw score annotation (useful when debug marker genes).
clf.data	classification data from 'getClassificationData'
score.info	cell type scores from 'getMarkerScoreInfo' function. Re-estimated if NULL
clusters	vector with cluster labels named by cell ids. Used to expand annotation on these clusters.
verbose	verbosity level (from 0 to 2)
max.depth	maximal depth for which annotation is done. Useful during manual marker selection
...	Arguments passed on to diffuseScorePerType

Value

list with parameters:

• annotation: annotation per level

• scores: assignment scores per level

• annotation.filt: the same as annotation, but cells, which don't pass QC are assigned to NA class

Examples

  clf_data <- getClassificationData(cm, marker_path)
  ann_by_level <- assignCellsByScores(graph, clf_data, clusters=clusters)

khodosevichlab/CellAnnotatoR documentation built on June 29, 2022, 9:12 p.m.