vargen_visualisation: Generate a plot of the variants on the OMIM genes

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Generate a plot of the variants on the OMIM genes

Description

The plot contains 4 tracks:

• The chromosome, with a red marker on the gene location

• The ensembl transcripts

• The variant consequences, grouped by type (eg: INTRONIC, STOP LOST etc...), each green bar represent a variant

• The cadd phred score, each dot represent a variant

Usage

vargen_visualisation(
  annotated_snps,
  outdir = "./",
  rsid_highlight,
  device = "pdf",
  verbose = FALSE,
  gene_mart
)

Arguments

annotated_snps	a data.frame from the merging of the outputs of vargen_pipeline and annotate_variants
outdir	the directory that will contain the plots
rsid_highlight	optional, a vector of rsids, which will be plotted in red on the cadd track.
device	only "pdf" and "png" are supported now.
verbose	if TRUE, will display progress messages
gene_mart	optional, a connection to ensembl gene mart, can be created using connect_to_gene_ensembl. If missing this function will be used to create the connection.

Value

nothing, create the plots in "outdir". One file per gene, the name format is <hgnc_symbol>_<ensembl_id>_GVIZ

Examples

vargen_install("./vargen_data/")

# Simple query
gene_mart <- connect_to_gene_ensembl()
DM1_simple <- vargen_pipeline(vargen_dir = "./vargen_data/", omim_morbid_ids = "222100",
                              fantom_corr = 0.25, outdir = "./", verbose = TRUE)

vargen_visualisation(annotated_snps = DM1_simple, verbose = TRUE,
                     outdir = "./DM1_gviz", device = "png",
                     gene_mart = gene_mart)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.