within_reference_pred: Predict cell type and return probabilities across all cell...

In xliu-uth/ImmClassifier: Knowledge-based and lineage-driven immune cell classification in single-cell RNA-Seq data

Predict cell type and return probabilities across all cell types within one training dataset

Description

Predict cell type and return probabilities across all cell types within one training dataset

Usage

within_reference_pred(queryfile.path, output.prefix = "query",
  num.cores = 1, mode = "run")

Arguments

mat	queryfile.path: string, path of the query dataset in tab-delimited text file with the rows as gene symbol, and columns as sampleID.
output.prefix:	string, the prefix of query dataset

Value

a list containing trained random forest model, prediction of training part and held-out part of reference dataset, prediction of query dataset, evaluation result using in training and test parts of the trainng dataset.

Examples

within_reference_pred(queryfile.path = "test/bulk.logrma.txt", output.prefix = "bulk", mode = "run")

xliu-uth/ImmClassifier documentation built on Sept. 5, 2022, 3:01 a.m.