ic_raw_to_tpm: ic_raw_to_tpm

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

ic_raw_to_tpm

Description

Transforms RNA-seq raw counts to TPM (Transcript Per kilobase Million).

Usage

ic_raw_to_tpm(counts, genes_id, biomart)

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'.
biomart	Data frame containing a biomaRt query with the following attributes: ensembl_gene_id, hgnc_symbol, entrezgene_id, transcript_length, refseq_mrna. In the case of mus musculus data, external_gene_name must be obtained and then change the column name for hgnc_symbol. Uploaded biomaRt queries in GEGVIC: 'ensembl_biomartGRCh37', ensembl_biomartGRCh38_p13' and 'ensembl_biomartGRCm38_p6', 'ensembl_biomartGRCm39'.

Value

Returns a matrix containing expression counts as TPM with HGNC gene symbols as rownames and samples identifiers as colnames.

Examples

tpm <- ic_raw_to_tpm(counts = sample_counts,
                     genes_id = 'ensembl_gene_id',
                     biomart = ensembl_biomart_GRCh38_p13)

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