Man pages for Bioconductor-mirror/AllelicImbalance
Investigates Allele Specific Expression

AllelicImbalance-packageA package meant to provide all basic functions for...
annotationBarplotadd annotation to AllelicImbalance barplot
annotation-wrappersAnnotationDb wrappers
ASEset-barplotbarplot ASEset objects
ASEset-classASEset objects
ASEset-filtersgenotype filter methods
ASEsetFromBamASEset from bam file
ASEset-gbarplotgbarplot ASEset objects
ASEset-glocationplotglocationplot ASEset objects
ASEset-gviztrackASEset-gviztrack ASEset objects
ASEset.oldASEset.old object
ASEset-scanForHeterozygotesscanForHeterozygotes
ASEset.simASEset.sim object
barplot-lattice-supportlattice barplot inner functions for ASEset objects
binom.testbinomial test
chisq.testchi-square test
cigar-utilitiesrealCigarPosition
countAllelesFromBamalleleCounts from bam file
coverageMatrixListFromGALcoverage matrix of GAlignmentsList
decorateWithExonsdecorateWithExons
decorateWithGenesdecorateWithGenes
defaultMapBiasGenerate default mapbias from genotype
defaultPhasedefaultPhase
detectAIdetectAI
DetectedAI-classDetectedAI class
DetectedAI-plotDetectedAI plot
DetectedAI-summaryDetectedAI summary
fractionPlotDfPlot Dataframe
gbaglobal analysis wrapper
genomatrixgenomatrix object
genotype2phasegenotype2phase
getAlleleCountssnp count data
getAlleleQualitysnp quality data
getAreaFromGeneNamesGet Gene Area
getDefaultMapBiasExpMeanMap Bias
getSnpIdFromLocationGet rsIDs from locations of SNP
GlobalAnalysis-classGlobalAnalysis class
GRvariantsGRvariants object
histplothistogram plots
implodeList-oldimplode list of arguments into environment
import-bamImport Bam
import-bam-2Import Bam-2
import-bcfImport Bcf Selection
inferAllelesinference of SNPs of ASEset
inferAltAlleleinferAltAllele
inferGenotypesinfererence of genotypes from ASEset count data
initialize-ASEsetInitialize ASEset
initialize-DetectedAIInitialize DetectedAI
initialize-GlobalAnalysisInitialize GlobalAnalysis
initialize-RiskVariantInitialize RiskVariant
legendBarplotadd legend to AllelicImbalance barplot
LinkVariantAlmlof-classLinkVariantAlmlof class
LinkVariantAlmlof-plotplot LinkVariantAlmlof objects
locationplotlocationplot ASEset objects
lvalva
lva.internallva.internal
makeMaskedFastamakes masked fasta reference
mapBiasRefmapBias for reference allele
minCountFiltminCountFilt methods
minFreqFiltminFreqFilt methods
multiAllelicFiltmulti-allelic filter methods
phase2genotypephase2genotype
phaseArray2phaseMatrixphaseArray2phaseMatrix
phaseMatrix2ArrayphaseMatrix2Array
randomRefRandom ref allele from genotype
readsreads object
refAlleleReference allele
regionSummaryregionSummary
RegionSummary-classRegionSummary class
RiskVariant-classRiskVariant class
scanForHeterozygotes-oldscanForHeterozygotes-old
Bioconductor-mirror/AllelicImbalance documentation built on July 1, 2017, 4:06 a.m.