select_vcf_fields: Select VCF fields

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Select VCF fields

Description

Select non-empty columns from each VCF field type.

Usage

select_vcf_fields(
  path,
  sampled_rows = 10000L,
  which = NULL,
  samples = NULL,
  nThread = 1,
  verbose = TRUE
)

Arguments

path	Path to local or remote VCF file.
sampled_rows	First N rows to sample. Set NULL to use full sumstats_file. when determining whether cols are empty.
which	Genomic ranges to be added if supplied. Default is NULL.
samples	Which samples to use: 1 : Only the first sample will be used (DEFAULT). NULL : All samples will be used. c("<sample_id1>","<sample_id2>",...) : Only user-selected samples will be used (case-insensitive).
nThread	Number of threads to use for parallel processes.
verbose	Print messages.

Value

ScanVcfParam object.

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.