Package: gwasglue2 0.0.0.9000

Rita Rasteiro

gwasglue2: GWAS summary data sources connected to analytical tools

Description: Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.

Authors:Gibran Hemani [aut], Rita Rasteiro [cre, aut], Christopher Woods [aut]

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gwasglue2.pdf |gwasglue2.html✨
gwasglue2/json (API)
NEWS

# Install 'gwasglue2' in R:
install.packages('gwasglue2', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mrcieu/gwasglue2/issues

On CRAN:

5.82 score 19 stars 3 packages 11 scripts 46 exports 16 dependencies

Last updated 12 months agofrom:c93b3a1fca. Checks:OK: 6 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winOKNov 22 2024
R-4.4-macOKNov 22 2024
R-4.3-winOKNov 22 2024
R-4.3-macNOTENov 22 2024

Exports:add_summarysetaddToMetadataassertSameShapeconvertForTwoSampleMRcreate_datasetcreate_dataset_from_tibblecreate_metadatacreate_summary_set_from_lbfcreate_summarysetcreate_summaryset_from_gwasvcfcreate_summaryset_from_tibbleDataSetdataset_to_hyprcolocdimDatadownload_chainfilegetAttributesgetDatagetLDMatrixgetLengthgetMetadatagetRSIDgetShapegetSummaryDatagetSummarySetgetTraitOrggetVariantsharmonise_ldharmoniseDataisHarmonisedisHarmonisedLDlbf_to_z_contliftovermerge_datasetsmeta_analysisoverlapVariantsplot_gwasgluesetAttributessetMetadatasetRSIDsetShapesetTraitOrgsetVariantidsetVariantssetZscoresSummarySetsusie_to_dataset

Dependencies:clidplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigR6rlangtibbletidyselectutf8vctrswithr

Strategy

Rendered fromStrategy.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-07-17
Started: 2022-11-23

Tutorial 1: How to create a SummarySet and a DataSet

Rendered fromSummarySet_DataSet.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-09-12
Started: 2023-07-17

Tutorial 2: MR analysis

Rendered frommr.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-07-17
Started: 2023-06-27

Tutorial 3: Regional genotype-phenotype map

Rendered fromfinemap_coloc1.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-07-17
Started: 2023-06-27

Tutorial 4: Meta analysis

Rendered frommeta.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-08-03
Started: 2023-06-13

Tutorial 5: Alternative regional genotype-phenotype map example, with meta-analyses included

Rendered fromfinemap_coloc2.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-08-03
Started: 2023-06-27

Tutorial 6: Remap genomic coordinates to a different genome assembly

Rendered fromliftover.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2023-08-08
Started: 2023-08-03

Readme and manuals

Help Manual

Help pageTopics
Add a SummarySet to a DataSetadd_summaryset
Add to metadata in the SummarySetaddToMetadata addToMetadata,SummarySet-method
Assert if the shapes of SummarySets in the gwasglue2 DataSet are the sameassertSameShape assertSameShape,DataSet-method
Convert tool to TwoSampleMR formatconvertForTwoSampleMR convertForTwoSampleMR,DataSet-method
Creates a DataSet object using gwasglue2 SummarySet objects, and harmonise data against datacreate_dataset
Creates a DataSet object using GWAS summary statistics, and harmonise data against datacreate_dataset_from_tibble
Metadata objectcreate_metadata
Create SummarySet from log Bayes Factorcreate_summary_set_from_lbf
A function to create a gwasglue2 SummarySet object from different sources and formatscreate_summaryset
A function to create a gwasglue2 SummarySet object from a vcf filecreate_summaryset_from_gwasvcf
A function to create a gwasglue2 SummarySet object from a tibblecreate_summaryset_from_tibble
DataSet to hyprcolocdataset_to_hyprcoloc
An S4 class to represent the Data SetDataSet DataSet-class
Dimensions of the GWAS Summary Statistics datadimData dimData,SummarySet-method
Chain files downloaderdownload_chainfile
Get Method to retrieve the attributes linked to the SummarySetgetAttributes getAttributes,SummarySet-method
Get Method to retrieve the GWAS Summary StatisticsgetData getData,DataSet-method
Get Method to retrieve the Linkage Disequilibrium matrixgetLDMatrix getLDMatrix,DataSet-method
Size of the DataSetgetLength getLength,DataSet-method
Get Method to retrieve the metadata stored in the SummarySetgetMetadata getMetadata,SummarySet-method
Get Method to retrieve RSID/variants stored in the SummarySetgetRSID getRSID,SummarySet-method
Get the Shape of the gwasglue2 objectsgetShape getShape,SummarySet-method
Get Method to retrieve the GWAS Summary Statistics from the SummarySetgetSummaryData getSummaryData,SummarySet-method
Get Method to retrieve the gwasglue2 SummarySet objectgetSummarySet getSummarySet,DataSet-method
Get the trait organisation of the gwasglue2 DataSetgetTraitOrg getTraitOrg,DataSet-method
Get Method to retrieve RSID/variants stored in the SummarySetgetVariants getVariants,SummarySet-method
Harmonise data against LD matrixharmonise_ld
Harmonise LD matrix against summary data (now it just looks for overlaped variants. The harmonisation is done in ld_matrix_local) harmonise_ld_dat() is based TwoSampleMR::harmonise_ld_dat()harmonise_ld_dat
Harmonise the alleles and effects between two summary setsharmoniseData harmoniseData,DataSet-method
Check if the DataSet is harmonisedisHarmonised isHarmonised,DataSet-method
Check if the DataSet is harmonised against LD matrixisHarmonisedLD isHarmonisedLD,DataSet-method
Convert log Bayes Factor to summary statslbf_to_z_cont
modified from ieugwasr::ld_matrix_local () Get LD matrix using local plink binary and reference datasetld_matrix_local
Remap genomic coordinates to a different genome assemblyliftover
Merge Datasetsmerge_datasets
Meta analysismeta_analysis
Look for overlapped variants between SummarySets in the DataSet and ResizeoverlapVariants overlapVariants,DataSet-method
Plotplot_gwasglue
Set Method to store the attributes of the SummarySetsetAttributes setAttributes,SummarySet-method
Set Method to add metadata to the SummarySetsetMetadata setMetadata,SummarySet-method
Set Method to store RSID/variants in the SummarySetsetRSID setRSID,SummarySet-method
Set the Shape of the gwasglue2 objectssetShape setShape,SummarySet-method
Set the trait organisation of the gwasglue2 DataSetsetTraitOrg setTraitOrg,DataSet-method
Set Method to create an internal Variant ID for the SummarySetsetVariantid setVariantid,SummarySet-method
Set Method to store RSID/variants in the SummarySetsetVariants setVariants,SummarySet-method
Calculating Z-scoressetZscores setZscores,DataSet-method
An S4 class to represent the Summary SetSummarySet-class
SusieR to DataSetsusie_to_dataset