AllelicImbalance-package | A package meant to provide all basic functions for high-throughput allele specific expression analysis |
alleleCounts | ASEset objects |
alleleCounts-method | ASEset objects |
alleleCounts<- | ASEset objects |
alleleCounts<--method | ASEset objects |
AllelicImbalance | A package meant to provide all basic functions for high-throughput allele specific expression analysis |
annotation-wrappers | AnnotationDb wrappers |
arank | ASEset objects |
arank-method | ASEset objects |
ASEDAnnotationTrack | ASEset-gviztrack ASEset objects |
ASEDAnnotationTrack-method | ASEset-gviztrack ASEset objects |
ASEset | ASEset objects |
ASEset-barplot | barplot ASEset objects |
ASEset-class | ASEset objects |
ASEset-glocationplot | glocationplot ASEset objects |
ASEset-gviztrack | ASEset-gviztrack ASEset objects |
ASEset-lbarplot | lbarplot ASEset objects |
ASEset-locationplot | locationplot ASEset objects |
ASEset.sim | ASEset.sim object |
ASEsetFromCountList | Initialize ASEset |
barplot | barplot ASEset objects |
barplot-lattice-support | lattice barplot inner functions for ASEset objects |
barplot-method | barplot ASEset objects |
barplotLatticeCounts | lattice barplot inner functions for ASEset objects |
barplotLatticeFraction | lattice barplot inner functions for ASEset objects |
binom.test | binomial test |
binom.test-method | binomial test |
boxplot | boxplots |
boxplot-method | boxplots |
chisq.test | chi-square test |
chisq.test-method | chi-square test |
countsPerSample | ASEset objects |
countsPerSample-method | ASEset objects |
countsPerSnp | ASEset objects |
countsPerSnp-method | ASEset objects |
CoverageDataTrack | ASEset-gviztrack ASEset objects |
CoverageDataTrack-method | ASEset-gviztrack ASEset objects |
coverageMatrixListFromGAL | coverage matrix of GAlignmentsList |
defaultMapBias | Generate default mapbias from genotype |
defaultMapBias-method | Generate default mapbias from genotype |
detectAI | detectAI |
detectAI-method | detectAI |
fraction | ASEset objects |
fraction-method | ASEset objects |
frequency | ASEset objects |
frequency-method | ASEset objects |
frequency-method | ReferenceBias class |
genofilters | genotype filter methods |
genotype | ASEset objects |
genotype-method | ASEset objects |
genotype<- | ASEset objects |
genotype<--method | ASEset objects |
getAlleleCounts | snp count data |
getAnnotationDataFrame | AnnotationDb wrappers |
getAreaFromGeneNames | Get Gene Area |
getCDSFromAnnotation | AnnotationDb wrappers |
getCDSVector | AnnotationDb wrappers |
getDefaultMapBiasExpMean | Map Bias |
getDefaultMapBiasExpMean3D | Map Bias |
getExonsFromAnnotation | AnnotationDb wrappers |
getExonsVector | AnnotationDb wrappers |
getGenesFromAnnotation | AnnotationDb wrappers |
getGenesVector | AnnotationDb wrappers |
getSnpIdFromLocation | Get rsIDs from locations of SNP |
getTranscriptsFromAnnotation | AnnotationDb wrappers |
getTranscriptsVector | AnnotationDb wrappers |
glocationplot | glocationplot ASEset objects |
glocationplot-method | glocationplot ASEset objects |
GRvariants | GRvariants object |
hetFilt | genotype filter methods |
hetFilt-method | genotype filter methods |
hetPerSample | ReferenceBias class |
hetPerSample-method | ReferenceBias class |
hetPerSnp | ReferenceBias class |
hetPerSnp-method | ReferenceBias class |
hist | histogram plots |
hist-method | histogram plots |
histplot | histogram plots |
impBamGAL | Import Bam |
impBamGRL | Import Bam |
impBcfGR | Import Bcf Selection |
impBcfGRL | Import Bcf Selection |
implodeList | implode list of arguments into environment |
import-bam | Import Bam |
import-bcf | Import Bcf Selection |
inferAlleles | inference of SNPs of ASEset |
inferAlleles-method | inference of SNPs of ASEset |
inferGenotypes | infererence of genotypes from ASEset count data |
inferGenotypes-method | infererence of genotypes from ASEset count data |
initialize-ASEset | Initialize ASEset |
initialize-ReferenceBias | Initialize ReferenceBias |
lbarplot | lbarplot ASEset objects |
lbarplot-method | lbarplot ASEset objects |
locationplot | locationplot ASEset objects |
locationplot-method | locationplot ASEset objects |
mapBias | ASEset objects |
mapBias-method | ASEset objects |
RBias | Initialize ReferenceBias |
reads | reads object |
refAllele | Reference allele |
refAllele-method | Reference allele |
refbiasByAnnotation | ReferenceBias class |
refbiasByAnnotation-method | ReferenceBias class |
ReferenceBias | ReferenceBias class |
ReferenceBias-class | ReferenceBias class |
ReferenceBias-method | ReferenceBias class |
ReferenceBias-show | genotype filter methods |
ReferenceBias-show-method | genotype filter methods |
refFraction | reference fraction |
refFraction-method | reference fraction |
scanForHeterozygotes | scanForHeterozygotes |
show-method | genotype filter methods |