sort_coordinates: Sort coordinates

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

Sort coordinates

Description

Sort a table of summary statistics by their genomic coordinates without reading the file into R.

Usage

sort_coordinates(
  target_path,
  chrom_col,
  start_col,
  end_col = start_col,
  comment_char = NULL,
  save_path = NULL,
  method = c("bash", "data.table"),
  outputs = c("command", "path", "data"),
  verbose = TRUE
)

Arguments

target_path	Path to full GWAS/QTL summary statistics file.
chrom_col	Name of the chromosome column in the target_path file.
start_col	Name of the genomic start position column in the target_path file.
end_col	Name of the genomic end position column in the target_path file.
comment_char	A single character which, when present as the first character in a line, indicates that the line is to be omitted from indexing.
save_path	File to save the results to.
method	Method to sort coordinates with.
outputs	"command"Text string of the command (without executing it.) "path"Path to the saved data file. "data"The resulting data in data.table format.
verbose	Print messages.

Source

sorting instructions

StackExchange discussion of how sort handles numbers

Examples

dat <- echodata::BST1
tmp <- tempfile()
data.table::fwrite(dat, tmp)
out <- echotabix::sort_coordinates(target_path=tmp, 
                                   chrom_col = "CHR", 
                                   start_col = "POS")

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.