Function reference • BioQC

All functions
`BaseIndexList-class`	An S4 class to hold a list of indices, with the possibility to specify the offset of the indices. IndexList and SignedIndexList extend this class
`GmtList-class`	An S4 class to hold geneset in the GMT file in a list, each item in the list is in in turn a list containing following items: name, desc, and genes.
`GmtList()`	Convert a list to a GmtList object
`IndexList-class`	An S4 class to hold a list of integers as indices, with the possibility to specify the offset of the indices
`IndexList()`	Convert a list to an IndexList object
`SignedGenesets-class`	An S4 class to hold signed genesets, each item in the list is in in turn a list containing following items: name, pos, and neg.
`SignedGenesets()`	Convert a list to a SignedGenesets object
`SignedIndexList-class`	An S4 class to hold a list of signed integers as indices, with the possibility to specify the offset of the indices
`SignedIndexList()`	Convert a list into a SignedIndexList
`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
`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 threshold
`getLeadingEdgeIndexFromVector()` `getLeadingEdgeIndexFromMatrix()`	Getting leading-edge indices from a vector
`gini()`	Calculate Gini Index of a numeric vector
`gmtlist2signedGenesets()`	Convert gmtlist into a list of signed genesets
`gsDesc()`	Gene-set descriptions
`gsGeneCount()` `gsSize()`	Gene-set gene counts
`gsGenes()`	Gene-set member genes
`gsName()`	Gene-set names
`gsNamespace()`	Gene-set namespaces
`hasNamespace()`	Whether namespace is set
`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<-`()	Set the offset of an `IndexList` or a `SignedIndexList` object
`offset()`	Get offset from an IndexList object
`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
`gsNamespace<-`()	gsNamespace<- is the synonym of setGsNamespace
`setNamespace()`	Set the namespace field in each gene-set within a GmtList
`show(<GmtList>)`	Show method for GmtList
`show(<IndexList>)`	Show method for IndexList
`show(<SignedGenesets>)`	Show method for SignedGenesets
`show(<SignedIndexList>)`	Show method for SignedIndexList
`simplifyMatrix()`	Simplify matrix in case of single row/columns
`[`(<GmtList>)	Subsetting GmtList object into another GmtList object
`[[`(<GmtList>)	Subsetting GmtList object to fetch one gene-set
`uniqGenesetsByNamespace()`	Make names of gene-sets unique by namespace, and member genes of gene-sets unique
`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 expression profiling data
`wmwTestInR()`	Wilcoxon-Mann-Whitney test in R

Reference

All functions