Man pages for nickb-/glida
A tool for visualisation and exploration of LD patterns

closeConnClose an existing connection to UCSC's public MySQL server
fromBiomaRtExtracts genes within region of interest from biomaRt. NOTE:...
fromUCSCEnsemblGenesFind all genes within a defined chromosomal region. Queries...
fromUCSCKnownGeneFind all genes within a defined chromosomal region. Queries...
fromUCSCRefGeneFind all genes within a defined chromosomal region. Queries...
geneAnnotationAdds gene annotations to an existing locus zoom, or ldZoom...
ldByRegionDownloads the 1000 Genomes data for the region of interest...
ldClusterClusters SNPs based on an LD dissimilarity matrix. Returns a...
ldDendrogramPerforms heirarchical clustering of LD dissimilarity matrix...
ldDissimilarityTakes a PLINK file containing pairwise R2 values between all...
ldDownloadDownloads a defined region from 1000 Genomes.
ldHeatmapProduces a heatmap based on an LD dissimilarity matrix.
ldPopulationRecursively extracts sample IDs from the 1000 Genomes panel...
ldProxyGiven a lead SNP, calculates LD of all other SNP (relative to...
ldProxyTableReads in the LD data (PLINK output) and returns an ordered...
ldReadRead an LD file generated by PLINK2
ldZoomProduces a locus zoom-like plot, where the y-axis is LD (R2)...
openConnEstablishes a connection to UCSC's public MySQL server
queryUCSCGiven an existing database connection, retrieve query results...
updatePositionsGiven a vector of RSIDs, query UCSC for updated chromosomal...
nickb-/glida documentation built on May 23, 2017, 2:43 p.m.