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