Man pages for genomation
Summary, annotation and visualization of genomic data

annotateWithFeatureFlank-methodsFunction to annotate a given GRanges object with...
annotateWithFeature-methodsFunction to annotate given GRanges object with a given...
annotateWithFeatures-methodsAnnotate given ranges with genomic features
annotateWithGeneParts-methodsAnnotate given object with promoter, exon, intron and...
annotatGrWithGenePartsannotatGrWithGeneParts function
AnnotationByFeature-classAn S4 class that information on overlap of target features...
AnnotationByGeneParts-classAn S4 class that information on overlap of target features...
AnnotationByGeneParts-methodsGet distance to nearest TSS and gene id from...
bed12ToExonsbed12ToExons function
bed12ToIntronsbed12ToIntrons function
binMatrix-methodsBins the columns of a matrix using a user provided function
binMaxFunction that computes a maximum value for each bin
binMeanFunction that computes a mean value for each bin
binMedianFunction that computes a median value for each bin
binMinFunction that computes a minimum value for each bin
binnerbinner function
binSumFunction that computes a sum of values in a bin
cageExample CAGE data set.
calculateOverlapSignificance-methodsfunction that calculates the significance of overlaps of two...
checkBedValiditycheckBedValidity function
checkClasscheckClass function
compressedAndUrl2tempcompressedAndUrl2temp function
constrainRangesconstrainRanges function
convertBed2Exons-methodsconvert a data frame read-in from a bed file to a GRanges...
convertBed2Introns-methodsconvert a data frame read-in from a bed file to a GRanges...
convertBedDf-methodsconvert a data frame read-in from a bed file to a GRanges...
cpgiExample CpG island data set.
c.ScoreMatrixc.ScoreMatrix
c.ScoreMatrixListc.ScoreMatrixList
detectUCSCheaderdetectUCSCheader function
distance2NearestFeaturedistance2NearestFeature function
enrichmentMatrix-ScoreMatrixList-methodCompute an enrichment of IP over control both stored in...
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-methodCompute an enrichment of IP (stored in ScoreMatrixList...
enrichmentMatrix-ScoreMatrix-methodCompute an enrichment of IP over control both stored in...
file.extfile.ext function
findFeatureComb-methodsFind combitations of genomic features
galpTo2RangesgalpTo2Ranges function
genesExample RefSeq genes data set.
getColorsgetColors function
getFeatsWithTargetsStats-methodsGet the percentage/count of annotation features overlapping...
getFlanks-methodsFunction to get upstream and downstream adjecent regions to a...
getMembers-methodsGet the membership slot of AnnotationByFeature
getRandomEnrichment-methodsget enrichment based on randomized feature overlap
getTargetAnnotationStats-methodsGet the percentage of target features overlapping with...
gffToGRangesConverts a gff formated data.frame into a GenomicRanges...
heatMatrixDraw a heatmap of a given ScoreMatrix object
heatMetaHeatmap for meta-region profiles
heatTargetAnnotation-methodsPlots the percentage of overlapping intervals with genomic...
intersectScoreMatrixList-methodsGet common rows from all matrices in a ScoreMatrixList object
listSliceMaxFunction creates a matrix storing data with desirable number...
listSliceMeanFunction creates a matrix storing data with desirable number...
listSliceMedianFunction creates a matrix storing data with desirable number...
listSliceMinFunction creates a matrix storing data with desirable number...
listSliceSumFunction creates a matrix storing data with desirable number...
Max_cFunction that computes a max value
Mean_cFunction that computes a mean value
Median_cFunction that computes a median value
Min_cFunction that computes a min value
multiHeatMatrixDraw multiple heatmaps from a ScoreMatrixList object
Ops-numeric-ScoreMatrixList-methodOps method for a ScoreMatrixList object. It enables to use...
Ops-ScoreMatrixList-numeric-methodOps method for a ScoreMatrixList object. It enables to use...
Ops-ScoreMatrixList-ScoreMatrixList-methodOps method for a ScoreMatrixList object. It enables to use...
Ops-ScoreMatrix-ScoreMatrix-methodOps method for a ScoreMatrix object. It enables to use...
orderBy-methodsReorder all elements of a ScoreMatrixList to a given ordering...
patternMatrix-methodsGet scores that correspond to k-mer or PWM matrix occurrence...
plotMetaLine plot(s) for meta-region profiles
plotTargetAnnotation-methodsPlot annotation categories from AnnotationByGeneParts or...
promotersExample promoter data set.
RandomEnrichment-classAn S4 class for storing 'getRandomEnrichment' function...
randomizeFeature-methodsfunction that randomizes the genomic coordinates
readBamreadBam function
readBedRead a BED file and convert it to GRanges.
readBigWigreadBigWig function
readBroadPeakA function to read the Encode formatted broad peak file into...
readFeatureFlank-methodsA function to read-in genomic features and their upstream and...
readGenericRead a tabular file and convert it to GRanges.
readNarrowPeakA function to read the Encode formatted narrowPeak file into...
readTableFastreadTableFast function
readTranscriptFeatures-methodsFunction for reading exon intron and promoter structure from...
read.zipread.zip function
scaleScoreMatrixListScale the ScoreMatrixList
scaleScoreMatrix-methodsScales the values in the matrix by rows and/or columns
ScoreMatrixBin-methodsGet bin score for bins on each window
ScoreMatrix-classAn S4 class for storing 'ScoreMatrix' function results
ScoreMatrixList-classAn S4 class for storing a set of 'ScoreMatrixList'
ScoreMatrixList-methodsMake ScoreMatrixList from multiple targets
ScoreMatrix-methodsGet base-pair score for bases in each window
show-methodsshow method for some of the genomation classes
sub-ScoreMatrix-ANY-ANY-ANY-methodExtract method for a ScoreMatrix object.
sub-ScoreMatrixList-ANY-ANY-ANY-methodExtract method for a ScoreMatrixList object.
Sum_cFunction that computes a sum value
target.typetarget.type function
genomation documentation built on Nov. 1, 2018, 2:12 a.m.