query_table_seqminer: Query tabular: 'seqminer'

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

Query tabular: seqminer

Description

Limitations of seqminer:

• Doesn't work with remote files.

• Assumes header column always starts with "#" (which is often incorrect) without the option for the user to specify otherwise. The only way that summary statistics can be used with seqminer is if they adhere to this convention, or were indexed using seqminer's tabix.createIndex function.

• Maintainers are unresponsive to requests for bug fixes.

Advantages of seqminer:

• tabix.read.table automatically converts query results to data.frame format (though this can now also be done by scanTabix_to_dt).

seqminer appears to be maintained to some degree (based on the latest commits), but the maintainers have been unresponsive to bug reports for years. This limits the consistent usability of seqminer.

Usage

query_table_seqminer(target_path, target_index, query_granges, 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.
verbose	Print messages.

Source

GitHub Issues: coordinate order error

GitHub Issues: remote file error

Lab contact details for seqminer maintainer

seqminer publication

seqminer2 publication (same package and GitHub repo, just updated)

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