Closed albert-ying closed 3 years ago
Hi @albert-ying,
Thank you for your suggestion! While we tried to make the mapping file all encompassing for summary statistics file headers and how people interpret them, I agree that it would be a good option to let the user input their own if required. To this end, I have included a mapping_file
parameter where the user can input their own mapping file in the same format as data(sumstatsColHeaders)
. This will be available in 1.1.6+ which should go live today, we are just incorporating a few more changes to this release.
Thanks, Alan.
v1.1.7 has been pushed to Github with this functionality in place. The functionality will propagate to Bioconductor in the next release around September.
Hi, just a suggestion: I think pre-defined column-name mapping is convenient but not very flexible. For example, I have a summary stats table with
a1
as effective allele anda0
as other allele. Theformat_sumstats
will, however, treata1
as reference allele anda0
as effective allele. I'll have to change the colnames of the file manually or update thesumstatsColHeaders
just for this dataset to get it to work.I think it would be better if the
format_sumstats
could take colnames mapping as the argument. For the example I showed, it would be much better if I can just do something like:or
Thank you!