Man pages for acidgenomics/AcidGenerics
Acid Genomics Generics
| AcidGenerics-package | AcidGenerics |
| aggregateCellsToSamples | Aggregate cells to samples |
| aggregateCols | Aggregate columns |
| aggregateRows | Aggregate rows |
| alphaSummary | Alpha level cutoff summary statistics |
| alphaThreshold | Alpha threshold |
| as.DataFrame | Coerce object to S4 DataFrame |
| as.DESeqDataSet | Coerce object to 'DESeqDataSet' |
| as.DESeqTransform | Coerce object to 'DESeqTransform' |
| as.DGEList | Coerce object to 'DGEList' |
| as.Seurat | Coerce object to Seurat |
| as.SingleCellExperiment | Coerce object to 'SingleCellExperiment' |
| as.SummarizedExperiment | Coerce object to SummarizedExperiment |
| atomize | Atomize |
| autopadZeros | Autopad zeros |
| barcodeRanksPerSample | Barcode ranks per sample |
| baseMeanThreshold | Base mean threshold |
| calculateMetrics | Calculate quality control metrics |
| camelCase | Camel case |
| capitalize | Capitalize |
| cast | Cast data from long to wide format |
| cellCountsPerCluster | Cell counts per cluster |
| cellsPerGeneFusion | Cells per gene fusion |
| cellsPerMutation | Cells per mutation |
| cellToSample | Cell-to-sample mappings |
| cellTypesPerCluster | Cell types per cluster |
| clusters | Cluster identifiers |
| coerceToList | Coerce to list |
| collapseToString | Collapse to string |
| collectionNames | Gene set collection names |
| contrastName | Contrast name |
| contrastNames | Contrast names |
| contrastSamples | Samples corresponding to a differential expression contrast |
| convertGenesToSymbols | Convert genes to symbols |
| convertSampleIdsToNames | Convert sample identifiers to names |
| convertSymbolsToGenes | Convert symbols to genes |
| convertToHuman | Convert data set by mapping to human orthologs |
| convertTranscriptsToGenes | Convert transcripts to genes |
| correlation | Correlation |
| cpm | Counts per million |
| deg | Differentially expressed genes |
| degIntersection | Intersection of differentially expressed genes |
| degPerContrast | Differentially expressed genes per contrast |
| diffExp | Differential expression |
| diffExpPerCluster | Differential expression per cluster |
| dottedCase | Dotted case |
| droplevels2 | Drop factor levels |
| encode | Encode using run-length encoding |
| enrichedGeneSets | Enriched gene sets |
| EnsemblToNcbi | Ensembl-to-NCBI gene identifier mappings |
| euclidean | Calculate Euclidean distance |
| excludeContaminatedCells | Exclude contaminated cells |
| excludeNonCancerCells | Exclude non-cancer cell lines |
| excludeNonHumanCells | Exclude non-human cell lines |
| excludeProblematicCells | Exclude problematic cells |
| export | Export data from R |
| factorize | Factorize |
| filterCells | Filter cells |
| filterNested | Keep rows that match a nested condition |
| findMarkers | Find cluster-specific marker genes |
| foldChangeToLogRatio | Fold change to log ratio |
| fpkm | Fragments per kilobase per million mapped fragments |
| geneFusions | Gene fusion pairs |
| geneIds | Gene identifiers |
| geneNames | Gene names |
| geneSet | Gene set |
| geneSetNames | Gene set names |
| geneSetResults | Gene set results |
| GeneToSymbol | Gene-to-symbol mappings |
| geometricMean | Geometric mean |
| headtail | Return the first and last parts of an object |
| humanize | Humanize an R object |
| import | Import data into R |
| integerCounts | Integer counts |
| interestingGroups | Interesting groups |
| intersectAll | Intersection of more than two vectors |
| intersectionMatrix | Intersection matrix |
| join | Join operations |
| kebabCase | Kebab case |
| keepOnlyAtomicCols | Keep only atomic columns |
| KnownMarkers | Known cell markers |
| leadingEdge | Leading edge genes |
| lfcShrink | Shrink log2 fold changes |
| lfcShrinkType | Shrunken log2 fold change (LFC) type |
| lfcThreshold | Log2 fold change threshold |
| logRatioToFoldChange | Log ratio to fold change |
| makeDimnames | Make syntactically valid dimnames |
| makeLabel | Make a plot axis or legend label out of a character string |
| makeNames | Make syntactically valid names |
| makeSampleData | Make sample data |
| makeTitle | Make a title out of character string |
| makeWords | Convert syntactic names to words separated by spaces |
| mapCells | Map input to cell identifiers |
| mapColnames | Map input to column names |
| mapGenes | Map input to gene identifiers |
| mapGenesToIds | Map genes (gene names) to gene identifiers |
| mapGenesToRownames | Map genes to row names |
| mapGenesToSymbols | Map genes (gene identifiers) to gene names (symbols) |
| mapRownames | Map input to row names |
| markdownPlots | Markdown plots |
| markdownTables | Markdown tables |
| matchAll | Match all positions of an argument |
| matchCellColumn | Match cell identifier column |
| matchGeneColumn | Match gene identifier column |
| matchNested | Match inside nested elements |
| matchRownameColumn | Match row name column |
| matchSampleColumn | Match sample identifier column |
| matchTranscriptColumn | Match transcript identifier column |
| melt | Melt data from wide to long format |
| metadata2 | Metadata |
| metrics | Quality control metrics |
| metricsPerSample | Quality control metrics per sample |
| mutate | Mutate multiple columns |
| mutations | Mutations |
| NcbiToEnsembl | NCBI-to-Ensembl gene identifier mappings |
| nesThreshold | Normalized enrichment score (NES) threshold |
| nonzeroRowsAndCols | Subset object to keep only non-zero rows and columns |
| plot5Prime3PrimeBias | Plot 5' to 3' bias |
| plotBarcodeRanks | Plot barcode ranks |
| plotBaseMean | Plot base mean distribution |
| plotCellCounts | Plot cell counts |
| plotCellCountsPerCluster | Plot cell counts per cluster |
| plotCells | Plot cells |
| plotCellTypesPerCluster | Plot cell types per cluster |
| plotCleveland | Cleveland plot |
| plotContrastScatter | Plot scatterplot of differential expression contrast |
| plotCorrelation | Correlation X-Y scatterplot |
| plotCorrelationHeatmap | Correlation heatmap |
| plotCountDensity | Plot count density |
| plotCounts | Plot counts |
| plotCountsCorrelation | Plot counts correlation |
| plotCountsCorrelationHeatmap | Plot counts correlation heatmap |
| plotCountsPerBiotype | Plot counts per biotype |
| plotCountsPerBroadClass | Plot counts per broad class definition |
| plotCountsPerCell | Plot counts per cell |
| plotCountsPerFeature | Plot counts per feature |
| plotCountsVsFeatures | Plot count and feature correlation |
| plotDegHeatmap | Differentially expressed gene heatmap |
| plotDegPca | Plot differentially expressed gene principal component... |
| plotDegStackedBar | Stacked bar plot of DEGs |
| plotDegUpset | UpSet plot of directional DEG intersections across contrasts |
| plotDots | Dot plot |
| plotEnrichedGeneSets | Plot enriched gene sets |
| plotEnrichedUpset | UpSet plot of directional enriched pathway intersections... |
| plotExonicMappingRate | Plot exonic mapping rate |
| plotFeature | Plot feature |
| plotFeatureSaturation | Plot feature (gene) detection saturation |
| plotFeaturesDetected | Plot features detected |
| plotFeaturesPerCell | Plot features per cell |
| plotGenderMarkers | Plot sexually dimorphic gender marker genes |
| plotGeneEffect | Plot gene effect |
| plotGeneEffectVsExpression | Plot gene effect vs. expression |
| plotGeneSet | Plot gene set enrichment |
| plotHeatmap | Heatmap |
| plotIntergenicMappingRate | Plot intergenic mapping rate |
| plotIntronicMappingRate | Plot intronic mapping rate |
| plotKnownMarkers | Plot known markers |
| plotLfc | Plot log2 fold change distributions |
| plotMa | MA plot |
| plotMappedReads | Plot mapped reads |
| plotMappingRate | Plot mapping rate |
| plotMarker | Plot cell-type-specific gene markers |
| plotMeanSd | Plot row standard deviations vs. row means |
| plotMitoRatio | Plot mitochondrial transcript abundance |
| plotMitoVsCoding | Plot mitochondrial vs. coding counts |
| plotNes | Plot normalized enrichment score |
| plotNovelty | Plot novelty score |
| plotPca | Principal component analysis plot |
| plotPcaCovariates | Find correlation between principal components (PCs) and... |
| plotPcElbow | Plot principal component elbow |
| plotPseudoVsAlignedCounts | Plot pseudo vs. aligned counts |
| plotQc | Quality control |
| plotQuantileHeatmap | Quantile heatmap |
| plotReadsPerCell | Plot read counts per cell |
| plotReducedDim | Plot reduced dimensions |
| plotRrnaMappingRate | Plot ribosomal RNA (rRNA) mapping rate |
| plotStackedBarPlot | Plot stacked bar plot |
| plotSums | Plot row or column sums |
| plotTopGeneEffectPerCell | Plot top gene effect per cell |
| plotTopGeneEffectPerGroup | Plot top gene effect per group |
| plotTopMarkers | Plot top markers |
| plotTotalCounts | Plot total read counts |
| plotTotalReads | Plot total reads |
| plotTsne | t-SNE plot |
| plotUmap | UMAP plot |
| plotUpset | UpSet plot |
| plotViolin | Violin plot |
| plotVolcano | Volcano plot |
| plotWaterfall | Plot waterfall |
| plotZerosVsDepth | Plot percentage of zeros vs. library depth |
| predictSensitivity | Predict sensitivity |
| rankedMatrix | Calculate a ranked matrix |
| rbindToDataFrame | Row bind elements 1:1 to a data frame |
| relativeLogExpression | Relative log expression |
| removeNa | Remove rows and columns containing only NA values |
| results | Results |
| resultsDiff | Relative difference of results |
| resultsMatrix | Results matrix |
| resultsNames | Results names |
| resultsTables | Results tables |
| sampleData | Sample data |
| sanitizeNa | Sanitize NA values |
| sanitizePercent | Sanitize percentage |
| select | Select multiple columns |
| selectCells | Select cells |
| selectSamples | Select samples |
| sem | Standard error of the mean |
| sentenceCase | Sentence case |
| showHeader | Header for object show method |
| slotAlignedCounts | Slot aligned counts |
| snakeCase | Snake case |
| splitByLevel | Split by factor level |
| standardizeCells | Standardize cell line names |
| stripExonVersions | Strip exon identifier versions |
| stripGeneVersions | Strip gene identifier versions |
| stripTranscriptVersions | Strip transcript identifier versions |
| subsetPerSample | Subset per sample |
| tmm | Trimmed mean of M-values |
| tnbc | Triple-negative breast cancer (TNBC) |
| topCellsPerSample | Top cells per sample |
| topMarkers | Top markers |
| tpm | Transcripts per million |
| transcriptIds | Transcript identifiers |
| transcriptNames | Transcript names |
| transformType | Variance-stabilizing transformation type |
| TxToGene | Transcript-to-gene mappings |
| unfactorize | Unfactorize |
| uniteInterestingGroups | Unite interesting groups into a single column |
| unlist2 | Flatten lists |
| unnest2 | Unnest a single list-column into expanded rows |
| upperCamelCase | Upper camel case |
| zerosVsDepth | Percentage of zeros vs. library depth |
| zscore | Calculate Z-score |
