preprocess_ge_counts: preprocess_ge_counts

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

preprocess_ge_counts

Description

Prepares RNA-seq raw counts for posterior analysis using DESeq2.

Usage

preprocess_ge_counts(counts, genes_id)

Arguments

counts	Data frame that contains gene expression data as raw counts.
genes_id	Name of the column that contains gene identifiers. Should be one of the following:'entrezgene_id', 'ensembl_gene_id' or 'hgnc_symbol'.

Value

Generates a data frame.

Examples

counts <- preprocess_ge_counts(counts = sample_counts,
                               genes_id = 'ensembl_gene_id')

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.