check_parent_child_coherence: Internal functions of scClassifR package

In grisslab/scClassifR: Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Description

Check label coherence in parent and child cell type in a Seurat object.

Check label coherence in parent and child cell type in a SingleCellExperiment object

Usage

## S4 method for signature 'Seurat'
check_parent_child_coherence(
  obj,
  pos_parent,
  parent_cell,
  cell_type,
  target_cell_type,
  tag_slot
)

## S4 method for signature 'SingleCellExperiment'
check_parent_child_coherence(
  obj,
  pos_parent,
  parent_cell,
  cell_type,
  target_cell_type,
  tag_slot
)

Arguments

obj	object
pos_parent	a vector indicating parent clf prediction
parent_cell	name of parent cell type
cell_type	name of cell type
target_cell_type	alternative cell types (in case of testing clf)
tag_slot	tag slot in SingleCellExperiment object indicating cell type

Value

TRUE if the classifier is valid or the reason why it is not

TRUE if the cell type is valid or the reason why it is not.

TRUE if the features is valid or the reason why it is not.

TRUE if the parent is valid or the reason why it is not.

TRUE if the p_thres is valid or the reason why it is not.

TRUE if the classifier is valid or the reason why it is not.

scClassifR object with the new parent.

scClassifR object with the new trained classifier.

scClassifR object with the new features.

a list of balanced count matrix and corresponding tags of balanced count matrix

the classification model (caret object)

row wise center-scaled count matrix

list of classifiers

filtered matrix

list of adjusted object and adjusted tag slot

adjusted Seurat object

adjusted SingleCellExperiment object

a binary vector for cell tag

list of cells which are positive to parent clf

prediction

simplified prediction

applicable matrix

clf performance

grisslab/scClassifR documentation built on Oct. 27, 2021, 12:13 p.m.