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 |
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 |
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 |
wmwTest()
|
Wilcoxon-Mann-Whitney rank sum test for high-throughput expression
profiling data |
wmwTestInR()
|
Wilcoxon-Mann-Whitney test in R |