get_best_snp_per_MB: Get the top SNP per 10 MB

In wuxi-nextcode/topR: Create custom plots for viewing genetic association results using ggplot

Description

get_best_snp_per_MB() Get the top SNP per 1 MB region All other input parameters are optional

Usage

get_best_snp_per_MB(
  df,
  thresh = 1e-09,
  region_size = 1e+06,
  protein_coding_only = FALSE,
  chr = NULL,
  .checked = FALSE,
  verbose = F
)

Arguments

df	Dataframe
thresh	P-value threshold, only consider variants with p-values below this threshold (1e-09 by default)
protein_coding_only	Set this variable to TRUE to only use protein_coding genes for annotation
chr	Use this argument to get the top variants from one chromosome only
.checked	If the input data has already been checked, this can be set to TRUE so it wont be checked again (FALSE by default)
region	Get the top/best variant (with p-value below thresh) within this region (region=1000000 by default)

Value

Dataframe of lead variants. Returns the best variant per MB (by default, change the region size with the region argument) with p-values below the input threshold (thresh=1e-09 by default)

Examples

## Not run: 
data(gwas_CD)
get_best_snp_per_MB(gwas_CD, thresh = 1e-09, region_size = 10000000)

## End(Not run)

wuxi-nextcode/topR documentation built on Dec. 23, 2021, 6:13 p.m.