query_table: Query a tabix file

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

Query a tabix file

Description

Query by genomic coordinates.

Usage

query_table(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  query_granges,
  query_method = c("rsamtools", "seqminer", "conda"),
  local = NULL,
  overlapping_only = FALSE,
  query_save = TRUE,
  save_path = tempfile(fileext = "tsv.gz"),
  cleanup_tbi = TRUE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

target_path	Path to tabix file.
target_index	Tabix index file for target_path.
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.
query_method	Method used for querying. See query for available options.
local	Whether target_path is stored locally or on a remote server/website. By default (NULL) will infer local status and use the appropriate query_method.
overlapping_only	Remove variants that do not overlap with the positions in query_dat.
query_save	Whether to save the queried data subset.
save_path	File path to save query subset to (as table).
cleanup_tbi	Remove local copies of tabix index file (.tbi) after completing queries.
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
nThread	Number of threads to use.
verbose	Print messages.

Value

data.table with the queried subset of genomic data.

See Also

Other tabix functions: construct_tabix_path(), construct_vcf_path(), convert(), index, query_vcf(), read_bgz(), run_bgzip()

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_table(
    target_path = tabix_files$path,
    query_dat = query_dat)

#### remote ####
target_path <- file.path(
    "https://egg2.wustl.edu/roadmap/data/byFileType",
    "chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final",
    "E099_15_coreMarks_dense.bed.bgz"
)
query_res2 <- echotabix::query_table(
    target_path = target_path,
    query_granges = query_dat) 

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