umap_analysis {TOmicsVis}

UMAP analysis for analyzing RNA-Seq data.

Description

UMAP analysis for analyzing RNA-Seq data.

Usage

umap_analysis(sample_gene, group_sample, seed = 1, method = "naive")

Arguments

sample_gene

Dataframe: gene expression dataframe (1st-col: Transcripts or Genes, 2nd-col~: Samples).

group_sample

Dataframe: Samples and groups for gene expression (1st-col: Samples, 2nd-col: Groups).

seed

Numeric: set seed for robust result. Default: 1.

method

Character: 'naive' (an implementation written in pure R) and 'umap-learn' (requires python package 'umap-learn').

Value

Table: UMAP analysis for analyzing RNA-Seq data.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_expression)
head(gene_expression)

data(samples_groups)
head(samples_groups)

# 3. Default parameters
res <- umap_analysis(gene_expression, samples_groups)
head(res)