query_table_conda: Query tabular: conda

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

Query tabular: conda

Description

Uses a conda-based installation of tabix instead of compiled C code from Rhtslib.

Usage

query_table_conda(
  target_path,
  target_index,
  query_granges,
  force = FALSE,
  preset = NULL,
  skip_lines = NULL,
  print_header = TRUE,
  use_regions_file = TRUE,
  conda_env = "echoR_mini",
  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.
force	Overwrite existing index without asking.
preset	gff, bed, sam, vcf.
skip_lines	skip first INT lines [0].
print_header	Print also the header lines.
use_regions_file	Specify query coordinates by writing them to a temporary file and supplying the file path to the "-R" argument.
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
verbose	Print messages.

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