read_vcf {MungeSumstats}R Documentation

Read in VCF format

Description

Read in VCF format

Usage

read_vcf(
  path,
  nThread = 1,
  temp_save = FALSE,
  keep_extra_cols = FALSE,
  save_path = tempfile(),
  nrows = Inf
)

Arguments

path

Filepath for the summary statistics file to be formatted. A dataframe or datatable of the summary statistics file can also be passed directly to MungeSumstats using the path parameter.

nThread

Number of threads to use for parallel processes.

temp_save

Save temprorary file before proceeding,

keep_extra_cols

Keep non-standard columns.

save_path

File path to save formatted data. Defaults to tempfile(fileext=".tsv.gz").

nrows

integer. The (maximal) number of lines to read. If Inf, will read in all rows.

Value

The modified sumstats_file


[Package MungeSumstats version 1.2.0 Index]