Skip to contents

Construct query

Source: R/construct_query.R
construct_query.Rd

Convert a data.table containing variant-level summary statistics into a GRanges object to be used for querying tabix-indexed files. Depending on the parameters supplied, the resulting GRanges object can contain one or more ranges, across one or more chromosomes.

Usage

construct_query(
  query_chrom = NULL,
  query_start_pos = NULL,
  query_end_pos = query_start_pos,
  query_dat = NULL,
  query_chrom_col = "CHR",
  query_start_col = "POS",
  query_end_col = query_start_col,
  query_snp_col = "SNP",
  standardise_colnames = FALSE,
  as_blocks = TRUE,
  style = c("NCBI", "UCSC"),
  samples = character(),
  as_string = FALSE,
  verbose = TRUE
)

Arguments

query_chrom

Which chromosome to query (e.g. 1 or "chr1").

query_start_pos

The first position to query.

query_end_pos

The last position to query.

query_dat

Variant-level summary statistics.

query_chrom_col

Name of the chromosome column in query_dat (e.g. "CHR").

query_start_col

Name of the starting genomic position column in query_dat (e.g. "POS","start").

query_end_col

Name of the ending genomic position column in query_dat (e.g. "POS","end"). Can be the same as query_start_col when query_dat only contains SNPs that span 1 base pair (bp) each.

query_snp_col

Name of the RSID or variant ID column (e.g. "SNP").

standardise_colnames

Automatically rename all columns to a standard nomenclature using standardise_header.

as_blocks

If TRUE (default), will query a single range per chromosome that covers all ranges requested plus anything in between.

style

Style to return GRanges in:

"NCBI":

Chromosome format: 1 (default)

"UCSC":

Chromosome format: "chr1"

Uses seqlevelsStyle.

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.

as_string

Convert a GRanges object to a concatenated string of coordinates (e.g. "chr4:70000-90000,chr10:200-150001"). This can be used for specifying which regions you want to query (e.g. when using tabix). Uses granges_to_string.

verbose

Print messages.

Value

GRanges or ScanVcfParam object.

Parameters sets

If you supply the Set 1 of parameters, you do not need to supply the Set 2 parameters (and vice versa). Extra Parameters apply to both Set 1 and Set 2.

Set 1:

query_chrom, query_start_pos, query_end_pos

Set 2:

query_dat, query_chrom_col, query_start_col, query_end_col, as_blocks

Extra Parameters:

style, samples, as_string, verbose

Examples

if (FALSE) { # \dontrun{
gr <- echotabix::construct_query(query_dat=echodata::BST1)
} # }