to_granges: To 'GRanges'

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

To GRanges

Description

Convert a data.table to GRanges.

Usage

to_granges(
  sumstats_dt,
  seqnames.field = "CHR",
  start.field = "BP",
  end.field = "BP",
  style = c("NCBI", "UCSC")
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS.
seqnames.field	A character vector of recognized names for the column in df that contains the chromosome name (a.k.a. sequence name) associated with each genomic range. Only the first name in seqnames.field that is found in colnames(df) is used. If no one is found, then an error is raised.
start.field	A character vector of recognized names for the column in df that contains the start positions of the genomic ranges. Only the first name in start.field that is found in colnames(df) is used. If no one is found, then an error is raised.
end.field	A character vector of recognized names for the column in df that contains the end positions of the genomic ranges. Only the first name in start.field that is found in colnames(df) is used. If no one is found, then an error is raised.
style	GRanges style to convert to, "NCBI" or "UCSC".

Value

GRanges object

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