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Convert and query

Source: R/convert_and_query.R
convert_and_query.Rd

If it is not tabix format already (determined by checking for a .tbi file of the same name in the same directory), the full summary statistics file is converted into tabix format for super fast querying. A query is then made using the min/max genomic positions to extract a locus-specific summary stats file.

Usage

convert_and_query(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  target_format = NULL,
  study_dir = NULL,
  target_chrom_col = "CHR",
  target_start_col = "POS",
  target_end_col = target_start_col,
  query_granges,
  samples = character(),
  query_save = TRUE,
  query_save_path = tempfile(fileext = ".gz"),
  target_genome = "GRCh37",
  query_genome = "GRCh37",
  convert_methods = list(sort_coordinates = "bash", run_bgzip = "Rsamtools", index =
    "Rsamtools"),
  query_method = c("rsamtools", "seqminer", "conda"),
  conda_env = "echoR_mini",
  convert_force_new = FALSE,
  query_force_new = FALSE,
  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".

study_dir

Path to study folder.

target_chrom_col

Name of the chromosome column in the target_path file.

target_start_col

Name of the genomic start position column in the target_path file.

target_end_col

Name of the genomic end position column in the target_path file.

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.

convert_methods

A named list containing methods to run each step with.

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.

convert_force_new

If the target_path is already in sorted/indexed tabix format, set convert_force_new=TRUE to re-convert it into tabix format.

query_force_new

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

nThread

Number of threads to use.

verbose

Print messages.

Value

data.table or VCF of requested subset of target_path.

See also

Other tabix: index_variantannotation()

Examples

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

query_res <- echotabix::convert_and_query(
    target_path = target_path,
    target_start_col = "BP",
    query_granges = query_dat,
    query_force_new = TRUE)
} # }