query: Query tabix

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

Query tabix

Description

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

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)

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