Sort coordinates

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
)

Source

sorting instructions

StackExchange discussion of how sort handles numbers

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.

Examples

if (FALSE) { # \dontrun{
dat <- echodata::BST1
tmp <- tempfile()
data.table::fwrite(dat, tmp)
out <- echotabix::sort_coordinates(target_path=tmp,
                                   chrom_col = "CHR",
                                   start_col = "POS")
} # }