read_symbol_to_id_map: Read marker symbol to identifier mappings

In mgi.report.reader: Read Mouse Genome Informatics Reports

Read marker symbol to identifier mappings

Description

read_symbol_to_id_map() reads MRK_List1.rpt data and returns an efficient data table to be used for marker symbol remapping to marker identifiers. Note that old symbols will be remapped to new symbols' ids, if applicable.

This function is memoised.

Usage

read_symbol_to_id_map(report_file = NULL, n_max = Inf)

Arguments

report_file	The path to a MRK_List1.rpt file. Leave this as NULL and the function will automatically download the report from https://www.informatics.jax.org/downloads/reports/MRK_List1.rpt.
n_max	Maximum number of lines to read.

Value

A data.table where each row is a mapping, from marker_symbol to marker_id_now:

• marker_symbol (set as key): marker symbol is a unique abbreviation of the marker name.

• marker_id_now: genetic marker identifier replacement. If the record pertains a marker_symbol that was withdrawn, then marker_id_now indicates the most recent in-use marker identifier that replaced it.

mgi.report.reader documentation built on Sept. 11, 2024, 8:41 p.m.