# Detect tissue heterogeneity in expression profiles with gene sets

## Documentation for package ‘BioQC’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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