Detect tissue heterogeneity in expression profiles with gene sets

Documentation for package ‘BioQC’ version 1.10.0

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absLog10p	Absolute base-10 logarithm of p-values
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 and related concepts
entropyDiversity	Shannon entropy and related concepts
entropySpecificity	Shannon entropy and related concepts
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
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
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-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	Shannon entropy and related concepts
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
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