README.md

In lbmountain/genevaR: Visualize gene structure and mark variants

Description

Plot a gene of interest with structure elements (exons and UTRs) and optionally add the positions of variants. \ \ A GFF data frame object (gff_file) is required as input containing the columns seqid, start, end, type and ID. Type specifies exon, three_prime_UTR and five_prime_UTR. \ To mark variants, a data frame (vcf_file) with the columns POS, ANN....GENEID and ANN....EFFECT is required. The gene IDs in ANN....GENEID should be similar to the ones used in the GFF file. ANN....EFFECT specifies the variant type. This file can be generated from a vcf file by using snpEFF to first split the vcf (vcfEffOnePerLine) and then SnpSift (extractFields) to filter for POS "ANN[*].GENEID" "ANN[*].EFFECT". \ Optionally the column Genotype can be added for use with the facets argument. \ \ Currently, genevaR is installed with the code:

devtools::install_github("lbmountain/genevaR")
library(genevaR)

lbmountain/genevaR documentation built on Dec. 21, 2021, 9:44 a.m.