scorePerCellUncertainty: Score Per Cell Uncertainty

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

Score Per Cell Uncertainty

Description

Score uncertainty per each cell

Usage

scorePerCellUncertainty(
  annotation,
  scores.norm,
  score.info,
  cur.types = unique(annotation),
  coverage.max.quantile = 0.75
)

Arguments

annotation	assigned annotation labels. Can be obtrained with 'assignCellsByScores'.
scores.norm	assignment scores. Can be obtrained with 'assignCellsByScores'.
score.info	list of marker scores per cell type. Can be obtained with 'getMarkerScoreInfo'
cur.types	subset of types used to measure uncertainty. Default: all values presented in annotation
coverage.max.quantile	all coverage values above this quantille are winsorized

Value

list of scores with elements:

• positive: uncertainty based on conflicting positive markers

• negative: uncertainty based on large expression of negative markers

• coverage: uncertainty based on low coverage

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