# basilisk and hail

## Documentation for package ‘BiocHail’ version 1.12.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

as.data.frame | S3 support
as.data.frame.default | S3 support
as.data.frame.hail.table.Table | convert hail.table.Table to R data frame
bare_hail | bare interface to hail using reticulate
colnames-method | extract field names from hail.table.Table
filter | s3 support
filter.hail.table.Table | filter rows of a hail Table
get_1kg | interface to 1kg import
get_key | S3 generic for get_key
get_key.hail.table.Table | S3 method for get_key
get_ukbb_sumstat_10kloci_mt | interface to a small subset of UKBB summary stats in MatrixTable format
hail_init | initialize hail, using more options
hail_init_simple | initialize hail
hail_stop | stop hail
kg_3202 | data.frame with metadata about 3202 samples genotyped against T2T reference
multipop_df | pheno_data component harvesting from columns of summary stats MatrixTable allowing for info on multiple populations in the pheno_data component
osn_1kg_path | Open Storage Network path to a zip of hail MatrixTable with some 1kg data for the Hail.is GWAS tutorial
osn_ukbb_sumst10k_path | Open Storage Network path to a zip of hail MatrixTable with a small subset of UKBB summary statistics as of 12/25/2022
path_1kg_annotations | generate path to installed annotations file
pcs_191k | HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
pcs_38k | HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
pheno_data_sec_2df | pheno_data component harvesting from columns of summary stats MatrixTable
rg_update | update the reference genome for a hail instance
rownames-method | acquire row names of a Hail Table, assuming key has been set
top2df | top-level annotation harvesting from columns of summary statistics MatrixTable
ukbb_init | initialize ukbb