R/get_genes_and_annotation.R
annotate_with_nearest_gene.Rdannotate_with_nearest_gene() Annotate the variant/snp with their nearest gene
Required parameters is a dataframe of SNPs (with the columns CHROM and POS)
annotate_with_nearest_gene(variants, protein_coding_only = FALSE, build = 38)a dataframe of variant positions (CHROM and POS)
Logical, if set to TRUE only annotate with protein coding genes (the default value is FALSE)
A number representing the genome build. Set to 37 to change to build (GRCh37). The default is build 38 (GRCh38).
the input dataframe with Gene_Symbol as an additional column
variants <-get_lead_snps(CD_UKBB)
annotate_with_nearest_gene(variants)
#> # A tibble: 9 × 10
#> CHROM POS ID REF ALT P OR AF Gene_Symbol biotype
#> <chr> <int> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 chr6 31660620 rs14884… T A 1.47e-24 2.43 0.0103 C6orf47 protei…
#> 2 chr16 50729867 rs20668… G GC 7.37e-24 2.14 0.0159 NOD2 protei…
#> 3 chr1 67216513 rs11576… G A 8.04e-20 0.777 0.441 C1orf141 protei…
#> 4 chr16 50485831 rs76176… A G 8.18e-16 1.75 0.0227 NKD1 protei…
#> 5 chr6 32708532 rs14461… A C 1.28e-15 1.80 0.0200 MTCO3P1 unproc…
#> 6 chr7 50274703 rs22193… T G 8.52e-14 1.23 0.593 IKZF1 protei…
#> 7 chr9 4984530 rs18874… G C 5.04e-11 0.833 0.633 JAK2 protei…
#> 8 chr5 40439961 rs77132… C T 7.43e-11 1.20 0.602 TTC33 protei…
#> 9 chr2 233237298 rs13418… A C 1.70e- 9 1.18 0.506 ATG16L1 protei…