Man pages for Accio/BioQC
Detect tissue heterogeneity in expression profiles with gene sets
| absLog10p | Absolute base-10 logarithm of p-values |
| appendGmtList | Append a GmtList object to another one |
| as.GmtList | Convert a list of gene symbols into a gmtlist |
| BaseIndexList-class | An S4 class to hold a list of indices, with the possibility... |
| entropy | Shannon entropy |
| entropyDiversity | Entropy-based sample diversity |
| entropySpecificity | Entropy-based gene-expression specificity |
| filterBySize | Filter a GmtList by size |
| filterPmat | Filter rows of p-value matrix under the significance... |
| getLeadingEdgeIndexFromVector | Getting leading-edge indices from a vector |
| gini | Calculate Gini Index of a numeric vector |
| GmtList | Convert a list to a GmtList object |
| gmtlist2signedGenesets | Convert gmtlist into a list of signed genesets |
| GmtList-class | An S4 class to hold geneset in the GMT file in a list, each... |
| gsDesc | Gene-set descriptions |
| gsGeneCount | Gene-set gene counts |
| gsGenes | Gene-set member genes |
| gsName | Gene-set names |
| gsNamespace | Gene-set namespaces |
| hasNamespace | Whether namespace is set |
| IndexList | Convert a list to an IndexList object |
| IndexList-class | An S4 class to hold a list of integers as indices, with the... |
| isValidBaseIndexList | Function to validate a BaseIndexList object |
| isValidGmtList | Function to validate a GmtList object |
| isValidIndexList | Function to validate an IndexList object |
| isValidSignedGenesets | Function to validate a SignedGenesets object |
| isValidSignedIndexList | Function to validate a SignedIndexList object |
| matchGenes | Match genes in a list-like object to a vector of genesymbols |
| offset | Get offset from an IndexList object |
| offset-set | Set the offset of an 'IndexList' or a 'SignedIndexList'... |
| prettySigNames | Prettify default signature names |
| readCurrentSignatures | Load current BioQC signatures |
| readGmt | Read in gene-sets from a GMT file |
| readSignedGmt | Read signed GMT files |
| sampleSpecialization | Entropy-based sample specialization |
| setDescAsNamespace | Set gene-set description as namespace |
| setGsNamespace | gsNamespace<- is the synonym of setGsNamespace |
| setNamespace | Set the namespace field in each gene-set within a GmtList |
| show-GmtList-method | Show method for GmtList |
| show-IndexList-method | Show method for IndexList |
| show-SignedGenesets-method | Show method for SignedGenesets |
| show-SignedIndexList-method | Show method for SignedIndexList |
| SignedGenesets | Convert a list to a SignedGenesets object |
| SignedGenesets-class | An S4 class to hold signed genesets, each item in the list is... |
| SignedIndexList | Convert a list into a SignedIndexList |
| SignedIndexList-class | An S4 class to hold a list of signed integers as indices,... |
| simplifyMatrix | Simplify matrix in case of single row/columns |
| sub-.GmtList | Subsetting GmtList object into another GmtList object |
| sub-sub-.GmtList | Subsetting GmtList object to fetch one gene-set |
| uniqGenesetsByNamespace | Make names of gene-sets unique by namespace, and member genes... |
| valTypes | prints the options of valTypes of wmwTest |
| wmwLeadingEdge | Identify BioQC leading-edge genes of one gene-set |
| wmwTest | Wilcoxon-Mann-Whitney rank sum test for high-throughput... |
| wmwTestInR | Wilcoxon-Mann-Whitney test in R |
