Man pages for isglobal-brge/dsOmics
DataSHIELD server site Omic functions
| addPhenoDataDS | Add Phenotype data to ExpressionSet |
| alleleFrequencyDS | Allelic frequency |
| BAM2VCF | Variant discovery on a BAM file |
| cellCountsDS | Estimate cell counts from methylation data |
| computeN | Compute N |
| createRSEDS | create a RangedSummarizedExperiment from a RNAseq count table... |
| DESeq2DS | Differential expression analysis on the server-side |
| dlaplace | Random laplace distribution generator |
| dot-fittedValues_exponential | Fit values for binomial model |
| dot-fittedValues_linear | Fit values for linear model |
| dot-one_hot_encoding | Create dummy variables |
| dot-retrievePGS | Internal function: Get PGS catalog table of polygenic risks |
| edgeRDS | Differential expression analysis on the server-side |
| EGAhtsgetResourceClient | EGA htsget resource client |
| EGAhtsgetResourceResolver | EGA htsget resource resolver |
| exactHWEDS | Hardy-Weinberg Equilibrium testing |
| extractPhenoFromGDSDS | Extract phenotype table from GenotypeData object |
| fastAlleleFrequencyDS | Allelic frequency |
| fastGWAS_ColSums | Get colsums needed for fast GWAS |
| fastGWAS_getFitted.values | Obtain fitted values given coefficients, family and values... |
| fastGWAS_getResiduals | Obtain residual values given fitted values, family and... |
| fastGWAS_PHENO_removeNAindiv | Remove individuals from the phenotype that have NAs on any of... |
| fastGWAS_S | Extract Geno iterator and Pheno information from GenotypeData... |
| fastGWAS_S_means | Get mean of the genotype by individual |
| featureDataDS | Retrieve information on features recorded in eSet-derived... |
| featureNamesDS | Retrieve feature names from eSets. |
| fvarLabelsDS | Retrieve names of annotation from eSets. |
| GA4GHResourceClient | GA4GH htsget server resource client |
| GA4GHResourceResolver | GA4GH htsget server resource resolver |
| GDSFileResourceClient | GDS file resource client |
| GDSFileResourceResolver | GDS file resource resolver |
| gdsSubset2 | Write a subset of data in a GDS file to a new GDS file |
| genoDimensionsDS | Get main dimensions of Genotype data |
| geno_pca_pooled_addPC2GenoDS | Add PCA results to the phenotype slot |
| geno_pca_pooled_addPCDS | Add PCA results to geno |
| GenotypeDataDS | Class GenotypeData. |
| getChromosomeNamesDS | Get names of chromosomes |
| getSNPSbyGenDS | Subset GDS with gene(s) |
| getVariable | Get slot of GDS object |
| GWASDS | Genome-wide association analysis (GWAS) on the server-side |
| Laplace_noise_generator | Random laplace generator |
| limmaDS | Differential expression analysis using limma on the... |
| limmaDS2 | Differential expression analysis using limma on the... |
| make_valid_namesDS | Rename column names and character variables |
| methylation_array_convertDS | Convert a Methylation ExpressionSet from EPIC to 450k Array |
| nFeaturesDS | Retrieve number of features from eSets and... |
| nSamplesDS | Retrieve number of samples from eSets and... |
| Opal2FileResourceGetter | Opal file resource getter |
| PCADS | Principal Component Analysis (PCA) on SNP genotype data |
| PCASNPSDS | Principal Component Analysis (PCA) on SNP genotype data |
| pDataDS | Retrieve information on experimental phenotypes recorded in... |
| plinkDS | Genome-wide association analysis (GWAS) using PLINK |
| plotPCADS | Grouping to plot PCA |
| plotPCASNPSDS | Grouping to plot PCA |
| PRSDS | Get Ploygenic Risk Score |
| PRSDS_aux | Auxiliary function to merge the PRS results to a table by ID |
| removeOutliersDS | Filter potential CpG outliers |
| rlaplace | Random laplace generator |
| RNAseqPreprocDS | Filter Genes By Expression Level |
| selFeatureDS | Subset the information of a given feature in a eSet object. |
| selSNPDS | Subset the information of a given SNP in a GDS object. |
| snptestDS | Interface to run SNPtest commands on a ssh connection (with... |
| subsetExpressionSet2DS | Subset ExpressionSet |
| subsetExpressionSetDS | Subset ExpressionSet |
| subsetGenoDS | Subset genotype |
| svdPartial | Partial singular value decomposition |
| varLabelsDS | Retrieve feature names from eSets. |
