ge_volcano: ge_volcano

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

ge_volcano

Description

Plots volcano plots from the outputs of the ge_annot() function.

Usage

ge_volcano(annot_res, fold_change = 2, p.adj = 0.05)

Arguments

annot_res	The output of ge_annot. List containing data frames of differential gene expression results between the different groups.
fold_change	An integer to define the fold change value to consider that a gene is differentially expressed.
p.adj	Numeric value to define the maximum adjusted p-value to consider that a gene is differentially expressed.

Value

Returns ggplot graphs.

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')
ge_volcano(annot_res = annot.res, fold_change = 2, p.adj = 0.05)

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