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]

gwasglue2_0.0.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gwasglue2/json (API)

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

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

On CRAN:

Conda:

5.48 score 24 stars 1 packages 12 scripts 46 exports 15 dependencies

Last updated from:c93b3a1fca. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK182
source / vignettesOK264
linux-release-x86_64OK161
macos-release-arm64OK132
macos-oldrel-arm64OK121
windows-develOK120
windows-releaseOK121
windows-oldrelOK125
wasm-releaseOK150

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:clidplyrgenericsgluelifecyclemagrittrpillarpkgconfigR6rlangtibbletidyselectutf8vctrswithr

Tutorial 1: How to create a SummarySet and a DataSet
SummarySet | Create a Summaryset from a GWAS vcf file | DataSet
Rendered fromSummarySet_DataSet.Rmdusingknitr::rmarkdown

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

Tutorial 6: Remap genomic coordinates to a different genome assembly
Rendered fromliftover.Rmdusingknitr::rmarkdown

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

Tutorial 4: Meta analysis
Rendered frommeta.Rmdusingknitr::rmarkdown

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

Tutorial 5: Alternative regional genotype-phenotype map example, with meta-analyses included
1. Setting the metadata | 2. HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) gene region | 2.1. Meta-analysis for the chd trait | 2.2. Creating a dataset for all the traits | 2.3. Finemapping with SusieR | 2.4. Colocolisation with hypercoloc | 3. PCSK9 (proprotein convertase subtilisin/kexin type 9) gene region | 3.1. Meta-analysis for the chd trait | 3.2. Creating a dataset for all the traits | 3.3. Finemapping with SusieR | 3.4. Colocolisation with hypercoloc | 4. NPC1L1 (NPC1 like intracellular cholesterol transporter 1) gene region | 4.1. Meta-analysis for the chd trait | 4.2. Creating a dataset for all the traits | 4.3. Finemapping with SusieR | 4.4. Colocolisation with hypercoloc | 5. LPA (Lipoprotein(A)) gene region | 5.1. Meta-analysis for the chd trait | 5.2. Creating a dataset for all the traits | 5.3. Finemapping with SusieR | 5.4. Colocolisation with hypercoloc
Rendered fromfinemap_coloc2.Rmdusingknitr::rmarkdown

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

Strategy
Objectives | Data structures | Work flow | Implementation | Controlled fields | Design | Variantid
Rendered fromStrategy.Rmdusingknitr::rmarkdown

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

Tutorial 2: MR analysis
Rendered frommr.Rmdusingknitr::rmarkdown

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

Tutorial 3: Regional genotype-phenotype map
Rendered fromfinemap_coloc1.Rmdusingknitr::rmarkdown

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

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