Function reference • gwasglue2

All functions

DataSet(): An S4 class to represent the Data Set

SummarySet-class: An S4 class to represent the Summary Set

addToMetadata(): Add to metadata in the SummarySet

add_summaryset(): Add a SummarySet to a DataSet

convertForTwoSampleMR(): Convert tool to TwoSampleMR format

create_dataset(): Creates a DataSet object using gwasglue2 SummarySet objects, and harmonise data against data

create_dataset_from_tibble(): Creates a DataSet object using GWAS summary statistics, and harmonise data against data

create_metadata(): Metadata object

create_summary_set_from_lbf(): Create SummarySet from log Bayes Factor

create_summaryset(): A function to create a gwasglue2 SummarySet object from different sources and formats

create_summaryset_from_gwasvcf(): A function to create a gwasglue2 SummarySet object from a vcf file

create_summaryset_from_tibble(): A function to create a gwasglue2 SummarySet object from a tibble

dataset_to_hyprcoloc(): DataSet to hyprcoloc

dimData(): Dimensions of the GWAS Summary Statistics data

download_chainfile(): Chain files downloader

getAttributes(): Get Method to retrieve the attributes linked to the SummarySet

getData(): Get Method to retrieve the GWAS Summary Statistics

getLDMatrix(): Get Method to retrieve the Linkage Disequilibrium matrix

getLength(): Size of the DataSet

getMetadata(): Get Method to retrieve the metadata stored in the SummarySet

getRSID(): Get Method to retrieve RSID/variants stored in the SummarySet

getSummaryData(): Get Method to retrieve the GWAS Summary Statistics from the SummarySet

getSummarySet(): Get Method to retrieve the gwasglue2 SummarySet object

getVariants(): Get Method to retrieve RSID/variants stored in the SummarySet

harmoniseData(): Harmonise the alleles and effects between two summary sets

harmonise_ld(): Harmonise data against LD matrix

harmonise_ld_dat(): 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()

isHarmonised(): Check if the DataSet is harmonised

isHarmonisedLD(): Check if the DataSet is harmonised against LD matrix

lbf_to_z_cont(): Convert log Bayes Factor to summary stats

ld_matrix_local(): modified from ieugwasr::ld_matrix_local () Get LD matrix using local plink binary and reference dataset

liftover(): Remap genomic coordinates to a different genome assembly

merge_datasets(): Merge Datasets

meta_analysis(): Meta analysis

overlapVariants(): Look for overlapped variants between SummarySets in the DataSet and Resize

plot_gwasglue(): Plot

setAttributes(): Set Method to store the attributes of the SummarySet

setMetadata(): Set Method to add metadata to the SummarySet

setRSID(): Set Method to store RSID/variants in the SummarySet

setVariantid(): Set Method to create an internal Variant ID for the SummarySet

setVariants(): Set Method to store RSID/variants in the SummarySet

setZscores(): Calculating Z-scores

susie_to_dataset(): SusieR to DataSet