Skip to contents

Query tabix

Source: R/query.R
query.Rd

Query a tabix table or VCF.

Usage

query(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  target_format = NULL,
  query_granges,
  samples = character(),
  query_save = TRUE,
  query_save_path = tempfile(fileext = ".gz"),
  target_genome = "GRCh37",
  query_genome = "GRCh37",
  query_method = c("rsamtools", "variantannotation", "conda", "seqminer"),
  conda_env = "echoR_mini",
  query_force_new = FALSE,
  as_datatable = TRUE,
  overlapping_only = FALSE,
  cleanup_tbi = TRUE,
  nThread = 1,
  verbose = TRUE
)

Arguments

target_path

Path to full GWAS/QTL summary statistics file.

target_index

Tabix index file for target_path.

target_format

Format of the target_path file: "vcf" or "table".

query_granges

GRanges object to be used for querying the target_path file. Alternatively, can be variant-level summary statistics to be converted into a GRanges object by construct_query.

samples

[Optional] Sample names to subset the VCF by. If this option is used, the GRanges object will be converted to a ScanVcfParam for usage by readVcf.

query_save

Whether to save the queried data subset.

query_save_path

Path to save retrieved query subset to.

target_genome

Genome build of the VCF file.

query_genome

Genome build that the query_granges is aligned to.

query_method

Method used for querying. See query for available options.

conda_env

Conda environments to search in. If NULL (default), will search all conda environments.

query_force_new

If the query subset (query_save_path) already exists, set query_force_new=TRUE to retrieve a new query subset.

as_datatable

Return the VCF subset file as a data.table (using vcf_to_dt). If save_path=TRUE the file will still be saved as a bgzip-compressed VCF file.

overlapping_only

Remove variants that do not overlap with the positions in query_dat.

cleanup_tbi

Remove local copies of tabix index file (.tbi) after completing queries.

nThread

Number of threads to use.

verbose

Print messages.

Examples

if (FALSE) { # \dontrun{
query_dat <- echodata::BST1

#### local ####
target_path <- echodata::example_fullSS()
tabix_files <- echotabix::convert(target_path = target_path,
                                  start_col = "BP")
query_res <- echotabix::query(
    target_path = tabix_files$path,
    query_granges = query_dat)
} # }