convert_and_query: Convert and query

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

Convert and query

Description

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

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) 

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