Detect tissue heterogeneity in expression profiles with gene sets

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Documentation for package ‘BioQC’ version 1.16.0

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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 to specify the offset of the indices. IndexList and SignedIndexList extend this class
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
GmtList Convert a list to a GmtList object
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.
gmtlist2signedGenesets Convert gmtlist into a list of signed genesets
gsDesc Gene-set descriptions
gsGeneCount Gene-set gene counts
gsGenes Gene-set member genes
gsName Gene-set names
gsNamespace Gene-set namespaces
gsNamespace<- gsNamespace<- is the synonym of setGsNamespace
gsSize Gene-set gene counts
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 possibility to specify the offset of the indices
IndexList-method Convert a list to an IndexList object
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
matchGenes-method Match genes in a list-like object to a vector of genesymbols
offset Get offset from an IndexList object
offset-method Get offset from an IndexList object
offset-set Set the offset of an 'IndexList' or a 'SignedIndexList' object
offset<- Set the offset of an 'IndexList' or a 'SignedIndexList' object
offset<--method Set the offset of an 'IndexList' or a 'SignedIndexList' 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
setNamespace Set the namespace field in each gene-set within a GmtList
show-method Show method for GmtList
show-method Show method for IndexList
show-method Show method for SignedGenesets
show-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 in in turn a list containing following items: name, pos, and neg.
SignedIndexList Convert a list into a SignedIndexList
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-method Convert a list into a SignedIndexList
simplifyMatrix Simplify matrix in case of single row/columns
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
wmwTest-method Wilcoxon-Mann-Whitney rank sum test for high-throughput expression profiling data
wmwTestInR Wilcoxon-Mann-Whitney test in R
[.GmtList Subsetting GmtList object into another GmtList object
[[.GmtList Subsetting GmtList object to fetch one gene-set