# Detect tissue heterogeneity in expression profiles with gene sets

## Documentation for package ‘BioQC’ version 1.22.0

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

## Help Pages

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
getLeadingEdgeIndexFromMatrix | Getting leading-edge indices from a vector
getLeadingEdgeIndexFromVector | Getting leading-edge indices from a vector
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
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
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
wmwLeadingEdge | Identify BioQC leading-edge genes of one gene-set
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