Man pages for BioQC
Detect tissue heterogeneity in expression profiles with gene sets

absLog10pAbsolute base-10 logarithm of p-values
appendGmtListAppend a GmtList object to another one
as.GmtListConvert a list of gene symbols into a gmtlist
BaseIndexList-classAn S4 class to hold a list of indices, with the possibility...
entropyShannon entropy
entropyDiversityEntropy-based sample diversity
entropySpecificityEntropy-based gene-expression specificity
filterBySizeFilter a GmtList by size
filterPmatFilter rows of p-value matrix under the significance...
giniCalculate Gini Index of a numeric vector
GmtListConvert a list to a GmtList object
gmtlist2signedGenesetsConvert gmtlist into a list of signed genesets
GmtList-classAn S4 class to hold geneset in the GMT file in a list, each...
gsDescGene-set descriptions
gsGeneCountGene-set gene counts
gsGenesGene-set member genes
gsNameGene-set names
gsNamespaceGene-set namespaces
hasNamespaceWhether namespace is set
IndexListConvert a list to an IndexList object
IndexList-classAn S4 class to hold a list of integers as indices, with the...
matchGenesMatch genes in a list-like object to a vector of genesymbols
offsetGet offset from an IndexList object
offset-setSet the offset of an 'IndexList' or a 'SignedIndexList'...
readGmtRead in gene-sets from a GMT file
readSignedGmtRead signed GMT files
sampleSpecializationEntropy-based sample specialization
setDescAsNamespaceSet gene-set description as namespace
setGsNamespacegsNamespace<- is the synonym of setGsNamespace
setNamespaceSet the namespace field in each gene-set within a GmtList
show-GmtList-methodShow method for GmtList
show-IndexList-methodShow method for IndexList
show-SignedGenesets-methodShow method for SignedGenesets
show-SignedIndexList-methodShow method for SignedIndexList
SignedGenesetsConvert a list to a SignedGenesets object
SignedGenesets-classAn S4 class to hold signed genesets, each item in the list is...
SignedIndexListConvert a list into a SignedIndexList
SignedIndexList-classAn S4 class to hold a list of signed integers as indices,...
simplifyMatrixSimplify matrix in case of single row/columns
sub-.GmtListSubsetting GmtList object into another GmtList object
sub-sub-.GmtListSubsetting GmtList object to fetch one gene-set
uniqGenesetsByNamespaceMake names of gene-sets unique by namespace, and member genes...
valTypesprints the options of valTypes of wmwTest
wmwTestWilcoxon-Mann-Whitney rank sum test for high-throughput...
wmwTestInRWilcoxon-Mann-Whitney test in R
BioQC documentation built on Oct. 31, 2019, 2:23 a.m.