Get the top SNP per 10 MB

Source: R/setters_and_getters.R

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

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

if (FALSE) {
data(gwas_CD)
get_best_snp_per_MB(gwas_CD, thresh = 1e-09, region_size = 10000000)
}