Perform LD clumping

Source: R/clump.r

<full description>

clump_gwasvcf(
  vcf,
  clump_kb = 1000,
  clump_r2 = 0.001,
  clump_p = 5e-08,
  pop = NULL,
  bfile = NULL,
  plink_bin = NULL,
  access_token = NULL
)

Arguments

vcf

VCF file or VCF object
clump_kb

Clumping kb window. Default is very strict, 10000
clump_r2

Clumping r2 threshold. Default is very strict, 0.001
clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)
pop

Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR. 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers
bfile

If this is provided then will use the API. Default = NULL
plink_bin

If null and bfile is not null then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL
access_token

Google OAuth2 access token. Used to authenticate level of access to data

Value

data frame of clumped results