Man pages for dyohanne/RepAn
Differential abundance Analysis for deep sequenced immune repertoire (Repseq) datasets
| addItemToObject | Adds new item to a repseq object |
| CDRepseqObj | Celiac disease (CD) PBMC Repseq data object |
| compareAbundanceInPairedSamplesForRanking | perform fisher's exact test based ranking of candidate DA... |
| compareClusterAbundancesPaired | compare cluster abundances for paired cases |
| compareClusterAbundancesUnPaired | compare cluster abundances for unpaired cases |
| computeVgeneEnrichement | V-gene usage analysis in differentially abundant CDR3s |
| cosineDist | cosine distance |
| CountkmerFrequency | Count kmer frequencies in a CDR3 |
| createDecoyCDR3s_V2 | Create decoy CDR3 sequences and add to each repertoire sample |
| determineWeight | Determine weight of kmer depending on position |
| extractDASubRepertoire | Extract DA subrepertoire and CDR3s contained in them |
| extractSubRepertoire | Extract any subrepertoire and CDR3s contained in them |
| findDAClonotypesInDACluster | Find out previously known Celiac disease CDR3s among DA... |
| findDAClusters | Find differentially abundant subrepertoires |
| findOptimalClusters | finds optimal clusters within samples and matches them across... |
| findOptimalK | Finding optimal number of clusters |
| getCenters | Compute cluster centroids |
| getClusterAbundancesTable | estimate the abundance of cluster of CDR3s |
| getClusterFoldChanges | subrepertoire fold change |
| getClusterLables | This function performs pairwise 4-mer nt usage clustering of... |
| getClusterMatches | find matching clusters of CDR3s |
| getDefined | Get CDR3s that have well defined V gene name from a... |
| getHasStop | Get stop codon containing CDR3s from a repertoire data... |
| getKmerFrequency | Count kmer frequencies in a CDR3 |
| getMatchingCluster | Find matching cluster |
| getOutOfFrame | Get out of frame CDR3s from a repertoire data (Repseq sample)... |
| getPooledSamples | Pool all repertoires |
| getProductive | Get productive only CDR3s from a repertoire data (Repseq... |
| getUnproductive | Get unproductive CDR3s from a repertoire data (Repseq sample)... |
| item.exists | check if item exists in repseq object |
| loadBioconductorPacks | Attaches packages from Bioconductor after installing them if... |
| loadPacks | Attaches packages from CRAN after installing them if they... |
| readSample | Read in Repertoire data (Repseq sample) in older Immunoseq... |
| readSampleV2 | Read in Repertoire data (Repseq sample) in the recent... |
| resampleReferenceSamples | Pool and resample samples to create reference/background... |
| runDaAnalysis | This function performs differential abundance analysis... |
| sampleFromPooled | Pool and resample samples to create reference/background... |
| sampleWithFeatuersFromPooled | Pool and resample samples to create reference/background... |
| scaleSamples | scale all samples to equal number of sequence reads |
| setUp | Setup repseq object for differential abudance analysis, CDR3... |
| shannonEntropy | normalized shannon entropy |
| TopDAClonotypes | Extract top differentially abundant CDR3 sequences |
