RenameBelowNode: In the CHETAH classification, replace the name of a Node and...

In jdekanter/CHETAH: Fast and accurate scRNA-seq cell type identification

Description

In the CHETAH classification, replace the name of a Node and all the names of the final and intermediate types under that Node.

Usage

RenameBelowNode(input, whichnode, replacement, nodes_exclude = NULL,
  types_exclude = NULL, node_only = FALSE, return_clas = FALSE)

Arguments

input	a SingleCellExperiment on which CHETAHclassifier has been run
whichnode	the number of the Node
replacement	a character vector that replaces the names under the selected Node
nodes_exclude	optional the names of the types that should NOT be replaced
types_exclude	optional numbers of the Nodes under the selected Node, that should NOT be replaced
node_only	only rename the Node itself, without affecting the types under that Node
return_clas	Instead of returning the SingleCellExperiment, only return the classification vector

Value

The SingleCellExperiment with the new classification or if 'return_clas = TRUE' the classification vector.

Examples

## In the example data replace all T-cell subtypes by "T cell"
input_mel <- RenameBelowNode(input = input_mel, whichnode = 7, replacement = "T cell")

jdekanter/CHETAH documentation built on Sept. 20, 2019, 3:31 a.m.