Man pages for isglobal-brge/dsOmics
DataSHIELD server site Omic functions

addPhenoDataDSAdd Phenotype data to ExpressionSet
alleleFrequencyDSAllelic frequency
BAM2VCFVariant discovery on a BAM file
cellCountsDSEstimate cell counts from methylation data
computeNCompute N
createRSEDScreate a RangedSummarizedExperiment from a RNAseq count table...
DESeq2DSDifferential expression analysis on the server-side
dlaplaceRandom laplace distribution generator
dot-fittedValues_exponentialFit values for binomial model
dot-fittedValues_linearFit values for linear model
dot-one_hot_encodingCreate dummy variables
dot-retrievePGSInternal function: Get PGS catalog table of polygenic risks
edgeRDSDifferential expression analysis on the server-side
EGAhtsgetResourceClientEGA htsget resource client
EGAhtsgetResourceResolverEGA htsget resource resolver
exactHWEDSHardy-Weinberg Equilibrium testing
extractPhenoFromGDSDSExtract phenotype table from GenotypeData object
fastAlleleFrequencyDSAllelic frequency
fastGWAS_ColSumsGet colsums needed for fast GWAS
fastGWAS_getFitted.valuesObtain fitted values given coefficients, family and values...
fastGWAS_getResidualsObtain residual values given fitted values, family and...
fastGWAS_PHENO_removeNAindivRemove individuals from the phenotype that have NAs on any of...
fastGWAS_SExtract Geno iterator and Pheno information from GenotypeData...
fastGWAS_S_meansGet mean of the genotype by individual
featureDataDSRetrieve information on features recorded in eSet-derived...
featureNamesDSRetrieve feature names from eSets.
fvarLabelsDSRetrieve names of annotation from eSets.
GA4GHResourceClientGA4GH htsget server resource client
GA4GHResourceResolverGA4GH htsget server resource resolver
GDSFileResourceClientGDS file resource client
GDSFileResourceResolverGDS file resource resolver
gdsSubset2Write a subset of data in a GDS file to a new GDS file
genoDimensionsDSGet main dimensions of Genotype data
geno_pca_pooled_addPC2GenoDSAdd PCA results to the phenotype slot
geno_pca_pooled_addPCDSAdd PCA results to geno
GenotypeDataDSClass GenotypeData.
getChromosomeNamesDSGet names of chromosomes
getSNPSbyGenDSSubset GDS with gene(s)
getVariableGet slot of GDS object
GWASDSGenome-wide association analysis (GWAS) on the server-side
Laplace_noise_generatorRandom laplace generator
limmaDSDifferential expression analysis using limma on the...
limmaDS2Differential expression analysis using limma on the...
make_valid_namesDSRename column names and character variables
methylation_array_convertDSConvert a Methylation ExpressionSet from EPIC to 450k Array
nFeaturesDSRetrieve number of features from eSets and...
nSamplesDSRetrieve number of samples from eSets and...
Opal2FileResourceGetterOpal file resource getter
PCADSPrincipal Component Analysis (PCA) on SNP genotype data
PCASNPSDSPrincipal Component Analysis (PCA) on SNP genotype data
pDataDSRetrieve information on experimental phenotypes recorded in...
plinkDSGenome-wide association analysis (GWAS) using PLINK
plotPCADSGrouping to plot PCA
plotPCASNPSDSGrouping to plot PCA
PRSDSGet Ploygenic Risk Score
PRSDS_auxAuxiliary function to merge the PRS results to a table by ID
removeOutliersDSFilter potential CpG outliers
rlaplaceRandom laplace generator
RNAseqPreprocDSFilter Genes By Expression Level
selFeatureDSSubset the information of a given feature in a eSet object.
selSNPDSSubset the information of a given SNP in a GDS object.
snptestDSInterface to run SNPtest commands on a ssh connection (with...
subsetExpressionSet2DSSubset ExpressionSet
subsetExpressionSetDSSubset ExpressionSet
subsetGenoDSSubset genotype
svdPartialPartial singular value decomposition
varLabelsDSRetrieve feature names from eSets.
isglobal-brge/dsOmics documentation built on Nov. 11, 2024, 4:18 a.m.