read_sumstats: Determine summary statistics file type and read them into...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Determine summary statistics file type and read them into memory

Description

Determine summary statistics file type and read them into memory

Usage

read_sumstats(
  path,
  nrows = Inf,
  standardise_headers = FALSE,
  samples = 1,
  sampled_rows = 10000L,
  nThread = 1,
  mapping_file = sumstatsColHeaders
)

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.
nrows	integer. The (maximal) number of lines to read. If Inf, will read in all rows.
standardise_headers	Standardise headers first.
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).
sampled_rows	First N rows to sample. Set NULL to use full sumstats_file. when determining whether cols are empty.
nThread	Number of threads to use for parallel processes.
mapping_file	MungeSumstats has a pre-defined column-name mapping file which should cover the most common column headers and their interpretations. However, if a column header that is in youf file is missing of the mapping we give is incorrect you can supply your own mapping file. Must be a 2 column dataframe with column names "Uncorrected" and "Corrected". See data(sumstatsColHeaders) for default mapping and necessary format.

Value

data.table of formatted summary statistics

Examples

path <- system.file("extdata", "eduAttainOkbay.txt",
    package = "MungeSumstats"
)
eduAttainOkbay <- read_sumstats(path = path)

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