get_genes_within_1Mb_of_signif_SNPs: Get genes within +/- 1Mb of significant SNPs

In RHReynolds/colochelpR: `colochelpR` is a home for helper functions for executing coloc

Get genes within +/- 1Mb of significant SNPs

Description

As colochelpR has primarily been used together with cis-eQTL datasets (where testing of SNP-gene associations is limited to genes within 1 Mb of the SNP), we define a region of +/- 1 Mb.

Usage

get_genes_within_1Mb_of_signif_SNPs(
  GWAS,
  pvalue_column,
  CHR_column,
  BP_column,
  pvalue_threshold = 5e-08,
  mart = 38
)

Arguments

GWAS	dataframe. Dataframe with GWAS results, containing, as a minimum, the following columns: (1) SNP identifier, (2) chromosome, in integer format, (3) basepair position, in integer format and (4) p-value column.
pvalue_column	chr. Name of column (in quotation marks) containing p-values in GWAS dataframe.
CHR_column	chr. Name of column (in quotation marks) containing chromosome name in GWAS dataframe.
BP_column	chr. Name of column (in quotation marks) containing basepair position in GWAS dataframe.
pvalue_threshold	num. P-value threshold for significance. Default value is 5e-8.
mart	int. Specify genome build.

Value

All genes within +/- 1Mb of significant SNPs.

RHReynolds/colochelpR documentation built on June 18, 2022, 5:53 a.m.