Man pages for isglobal-brge/dsOmicsClient
DataSHIELD client site Omics association functions.
| checkForExpressionSet | Check if object exists on the study server and if it's an... |
| dot-eafPlot | Auxiliary function for 'eafPlot' |
| dot-pzPlotgg | Auxiliary function for 'pzPlot' |
| ds.addPhenoData2eSet | Add Phenotype data to ExpressionSet |
| ds.alleleFrequency | Allelic frequency |
| ds.createRSE | Create a RangedSummarizedExperiment from a RNAseq count table... |
| ds.DESeq2 | Server-side Differential Gene Expression analysis using... |
| ds.edgeR | Server-side Differential Expression Analysis using edgeR |
| ds.exactHWE | Hardy-Weinberg Equilibrium testing |
| ds.fastGWAS | Fast genome-wide association analysis (GWAS) |
| ds.featureData | Retrieve information on features from eSets and RSEs. |
| ds.featureNames | Retrieve feature names from eSets and RSEs. |
| ds.fvarLabels | Retrieve phenotypic data (e.g. covariates) from eSets and... |
| ds.genoDimensions | Get main dimensions of Genotype data |
| ds.GenotypeData | Creates a GenotypeData object at each server |
| ds.getChromosomeNames | Get names of chromosomes |
| ds.getSNPs | Retrieve SNPs from |
| ds.getSNPSbyGen | Subset GDS with gene(s) |
| ds.glmSNP | Logistic regression analysis of pooled data for each SNP site... |
| ds.index.gdsn | Retrieve phenotypic data (e.g. covariates) from eSets. |
| ds.limma | Server-side Differential Gene Expression analysis using limma |
| ds.lmFeature | Linear regression analysis of pooled data for each CpG site... |
| ds.make_valid_names | Rename column names and character variables |
| ds.metaGWAS | Genome-wide association analysis (GWAS) |
| ds.methylation_array_convert | Convert a Methylation ExpressionSet from EPIC to 450k Array... |
| ds.nFeatures | Retrieve the number of features for eSets and RSEs. |
| ds.nSamples | Retrieve the number of samples for eSets and RSEs. |
| ds.PCA | Principal Component Analysis (PCA) on SNP genotype data |
| ds.PCASNPS | Principal Component Analysis (PCA) on SNP genotype data |
| ds.pData | Retrieve information on experimental phenotypes recorded in... |
| ds.PLINK | Genome-wide association analysis (GWAS) using PLINK |
| ds.PRS | Get Ploygenic Risk Score |
| ds.removeOutliers | Filter potential CpG outliers |
| ds.RNAseqPreproc | Filter Genes By Expression Level |
| ds.snptest | Interface to run SNPtest commands on a ssh connection (with... |
| ds.subsetExpressionSet | Subset ExpressionSet |
| ds.table_gds | Contingency tables of phenotypes |
| ds.varLabels | Retrieve phenotypic data (e.g. covariates) from eSets. |
| eafPlot | EAF plot |
| get_EGA_url | Get EGA URL |
| get_ga4gh_url | Get GA4GH URL |
| glmSNP | Fits a GLM to assess association between the outcome (binary... |
| lambdaNPlot | Lambda-N plot |
| lmFeature | Fits a LM to assess association between the features... |
| LocusZoom | LocusZoom |
| manhattan | Mannhattan Plot |
| metaBetaValues | Meta-analysis of beta values |
| metaPvalues | Meta-analysis of p-values |
| plot.dsLmFeature | Generate a QQ-plot of p-values output from any omic data... |
| plotPCA | Plot the results of a 'ds.PCA()' |
| plotPCASNPS | Plot the results of a 'ds.PCASNPS()' |
| pzPlot | P-Z plot |
| qqplot | Create a quantile-quantile plot with ggplot2. |
| seNPlot | SE-N Plot |
| standardizeGenoData | Get standaridization coefficients of Genotype data |
| tolist | PLINK arguments in the DataSHIELD required format |
