Package: BiocHail 1.7.1

Vincent Carey

BiocHail: basilisk and hail

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

Authors:Vincent Carey [aut, cre]

BiocHail_1.7.1.tar.gz
BiocHail_1.7.1.zip(r-4.5)BiocHail_1.7.1.zip(r-4.4)BiocHail_1.7.1.zip(r-4.3)
BiocHail_1.7.1.tgz(r-4.4-any)BiocHail_1.7.1.tgz(r-4.3-any)
BiocHail_1.7.1.tar.gz(r-4.5-noble)BiocHail_1.7.1.tar.gz(r-4.4-noble)
BiocHail_1.7.1.tgz(r-4.4-emscripten)BiocHail_1.7.1.tgz(r-4.3-emscripten)
BiocHail.pdf |BiocHail.html✨
BiocHail/json (API)
NEWS

# Install 'BiocHail' in R:
install.packages('BiocHail', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vjcitn/biochail/issues

Datasets:
  • kg_3202 - Data.frame with metadata about 3202 samples genotyped against T2T reference
  • 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

On BioConductor:BiocHail-1.7.1(bioc 3.21)BiocHail-1.6.0(bioc 3.20)

infrastructurebioconductorgeneticshail

6.01 score 6 stars 19 scripts 85 downloads 17 exports 53 dependencies

Last updated 1 months agofrom:3bfea67102. Checks:OK: 1 NOTE: 3 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winERRORDec 21 2024
R-4.5-linuxNOTEDec 21 2024
R-4.4-winERRORDec 21 2024
R-4.4-macNOTEDec 21 2024
R-4.3-winERRORDec 21 2024
R-4.3-macNOTEDec 21 2024

Exports:as.data.framebare_hailcolnamesfilterget_1kgget_keyget_ukbb_sumstat_10kloci_mthail_inithail_init_simplehail_stopmultipop_dfosn_1kg_pathosn_ukbb_sumst10k_pathpath_1kg_annotationsrg_updaterownamesukbb_init

Dependencies:askpassbasiliskbasilisk.utilsBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdir.expirydplyrfansifastmapfilelockgenericsglueherehttrjsonlitelatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootRSQLitestringistringrsystibbletidyrtidyselectutf8vctrswithr

01 BiocHail -- GWAS tutorial from hail.is

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromgwas_tut.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2023-09-02
Started: 2023-03-02

02 Working with larger VCF: T2T by chromosome

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromlarge_t2t.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2023-06-05
Started: 2023-03-02

03 Working with UK Biobank summary statistics

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromukbb.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2023-09-02
Started: 2023-03-02

Readme and manuals

Help Manual

Help pageTopics
S3 supportas.data.frame
S3 supportas.data.frame.default
convert hail.table.Table to R data frameas.data.frame.hail.table.Table
bare interface to hail using reticulatebare_hail
extract field names from hail.table.Tablecolnames,hail.table.Table-method
s3 supportfilter
filter rows of a hail Tablefilter.hail.table.Table
interface to 1kg importget_1kg
S3 generic for get_keyget_key
S3 method for get_keyget_key.hail.table.Table
interface to a small subset of UKBB summary stats in MatrixTable formatget_ukbb_sumstat_10kloci_mt
initialize hail, using more optionshail_init
initialize hailhail_init_simple
stop hailhail_stop
data.frame with metadata about 3202 samples genotyped against T2T referencekg_3202
pheno_data component harvesting from columns of summary stats MatrixTable allowing for info on multiple populations in the pheno_data componentmultipop_df
Open Storage Network path to a zip of hail MatrixTable with some 1kg data for the Hail.is GWAS tutorialosn_1kg_path
Open Storage Network path to a zip of hail MatrixTable with a small subset of UKBB summary statistics as of 12/25/2022osn_ukbb_sumst10k_path
generate path to installed annotations filepath_1kg_annotations
HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere referencepcs_191k
HWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere referencepcs_38k
pheno_data component harvesting from columns of summary stats MatrixTablepheno_data_sec_2df
update the reference genome for a hail instancerg_update
acquire row names of a Hail Table, assuming key has been setrownames,hail.table.Table-method
top-level annotation harvesting from columns of summary statistics MatrixTabletop2df
initialize ukbbukbb_init