Man pages for genomation
Summary, annotation and visualization of genomic data
| annotateWithFeatureFlank-methods | Function to annotate a given GRanges object with... |
| annotateWithFeature-methods | Function to annotate given GRanges object with a given... |
| annotateWithFeatures-methods | Annotate given ranges with genomic features |
| annotateWithGeneParts-methods | Annotate given object with promoter, exon, intron and... |
| annotatGrWithGeneParts | annotatGrWithGeneParts function |
| AnnotationByFeature-class | An S4 class that information on overlap of target features... |
| AnnotationByGeneParts-class | An S4 class that information on overlap of target features... |
| AnnotationByGeneParts-methods | Get distance to nearest TSS and gene id from... |
| bed12ToExons | bed12ToExons function |
| bed12ToIntrons | bed12ToIntrons function |
| binMatrix-methods | Bins the columns of a matrix using a user provided function |
| binMax | Function that computes a maximum value for each bin |
| binMean | Function that computes a mean value for each bin |
| binMedian | Function that computes a median value for each bin |
| binMin | Function that computes a minimum value for each bin |
| binner | binner function |
| binSum | Function that computes a sum of values in a bin |
| cage | Example CAGE data set. |
| calculateOverlapSignificance-methods | function that calculates the significance of overlaps of two... |
| checkBedValidity | checkBedValidity function |
| checkClass | checkClass function |
| compressedAndUrl2temp | compressedAndUrl2temp function |
| constrainRanges | constrainRanges function |
| convertBed2Exons-methods | convert a data frame read-in from a bed file to a GRanges... |
| convertBed2Introns-methods | convert a data frame read-in from a bed file to a GRanges... |
| convertBedDf-methods | convert a data frame read-in from a bed file to a GRanges... |
| cpgi | Example CpG island data set. |
| c.ScoreMatrix | c.ScoreMatrix |
| c.ScoreMatrixList | c.ScoreMatrixList |
| detectUCSCheader | detectUCSCheader function |
| distance2NearestFeature | distance2NearestFeature function |
| enrichmentMatrix-ScoreMatrixList-method | Compute an enrichment of IP over control both stored in... |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | Compute an enrichment of IP (stored in ScoreMatrixList... |
| enrichmentMatrix-ScoreMatrix-method | Compute an enrichment of IP over control both stored in... |
| file.ext | file.ext function |
| findFeatureComb-methods | Find combitations of genomic features |
| galpTo2Ranges | galpTo2Ranges function |
| genes | Example RefSeq genes data set. |
| getColors | getColors function |
| getFeatsWithTargetsStats-methods | Get the percentage/count of annotation features overlapping... |
| getFlanks-methods | Function to get upstream and downstream adjecent regions to a... |
| getMembers-methods | Get the membership slot of AnnotationByFeature |
| getRandomEnrichment-methods | get enrichment based on randomized feature overlap |
| getTargetAnnotationStats-methods | Get the percentage of target features overlapping with... |
| gffToGRanges | Converts a gff formated data.frame into a GenomicRanges... |
| heatMatrix | Draw a heatmap of a given ScoreMatrix object |
| heatMeta | Heatmap for meta-region profiles |
| heatTargetAnnotation-methods | Plots the percentage of overlapping intervals with genomic... |
| intersectScoreMatrixList-methods | Get common rows from all matrices in a ScoreMatrixList object |
| listSliceMax | Function creates a matrix storing data with desirable number... |
| listSliceMean | Function creates a matrix storing data with desirable number... |
| listSliceMedian | Function creates a matrix storing data with desirable number... |
| listSliceMin | Function creates a matrix storing data with desirable number... |
| listSliceSum | Function creates a matrix storing data with desirable number... |
| Max_c | Function that computes a max value |
| Mean_c | Function that computes a mean value |
| Median_c | Function that computes a median value |
| Min_c | Function that computes a min value |
| multiHeatMatrix | Draw multiple heatmaps from a ScoreMatrixList object |
| Ops-numeric-ScoreMatrixList-method | Ops method for a ScoreMatrixList object. It enables to use... |
| Ops-ScoreMatrixList-numeric-method | Ops method for a ScoreMatrixList object. It enables to use... |
| Ops-ScoreMatrixList-ScoreMatrixList-method | Ops method for a ScoreMatrixList object. It enables to use... |
| Ops-ScoreMatrix-ScoreMatrix-method | Ops method for a ScoreMatrix object. It enables to use... |
| orderBy-methods | Reorder all elements of a ScoreMatrixList to a given ordering... |
| patternMatrix-methods | Get scores that correspond to k-mer or PWM matrix occurrence... |
| plotMeta | Line plot(s) for meta-region profiles |
| plotTargetAnnotation-methods | Plot annotation categories from AnnotationByGeneParts or... |
| promoters | Example promoter data set. |
| RandomEnrichment-class | An S4 class for storing 'getRandomEnrichment' function... |
| randomizeFeature-methods | function that randomizes the genomic coordinates |
| readBam | readBam function |
| readBed | Read a BED file and convert it to GRanges. |
| readBigWig | readBigWig function |
| readBroadPeak | A function to read the Encode formatted broad peak file into... |
| readFeatureFlank-methods | A function to read-in genomic features and their upstream and... |
| readGeneric | Read a tabular file and convert it to GRanges. |
| readNarrowPeak | A function to read the Encode formatted narrowPeak file into... |
| readTableFast | readTableFast function |
| readTranscriptFeatures-methods | Function for reading exon intron and promoter structure from... |
| read.zip | read.zip function |
| scaleScoreMatrixList | Scale the ScoreMatrixList |
| scaleScoreMatrix-methods | Scales the values in the matrix by rows and/or columns |
| ScoreMatrixBin-methods | Get bin score for bins on each window |
| ScoreMatrix-class | An S4 class for storing 'ScoreMatrix' function results |
| ScoreMatrixList-class | An S4 class for storing a set of 'ScoreMatrixList' |
| ScoreMatrixList-methods | Make ScoreMatrixList from multiple targets |
| ScoreMatrix-methods | Get base-pair score for bases in each window |
| show-methods | show method for some of the genomation classes |
| sub-ScoreMatrix-ANY-ANY-ANY-method | Extract method for a ScoreMatrix object. |
| sub-ScoreMatrixList-ANY-ANY-ANY-method | Extract method for a ScoreMatrixList object. |
| Sum_c | Function that computes a sum value |
| target.type | target.type function |
