ge_annot: ge_annot

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

ge_annot

Description

Associates Entrez_gene_id (NCBI-ID) or ENSEMBL_gene_id to HGNC symbols (Hugo Gene Nomenclature Committee nomenclature).

Usage

ge_annot(results_dds, genes_id, biomart)

Arguments

results_dds	The output of the ge_diff_exp function. List containing data frames of differential gene expression results between the different groups.
genes_id	Name of the column that contains gene identifiers. Should be one of the following: 'ensembl_gene_id', 'entrezgene_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 list of data frames containing differential gene expression results, one for each level comparison where genes have been annotated using HGNC symbols.

Examples

results.dds <- ge_diff_exp(counts = sample_counts,
                           genes_id = 'ensembl_gene_id',
                           metadata = sample_metadata,
                           design = 'MSI_status',
                           ref_level = c('MSI_status', 'MSS'),
                           shrink = 'apeglm')
annot.res <- ge_annot(results_dds = results_dds,
                      genes_id = 'ensembl_gene_id',
                      biomart = ensembl_biomart_GRCh38_p13)

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