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

Description Usage Arguments Value Examples

View source: R/Utils_CHETAH.R

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

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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

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## 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.