An S4 class that information on overlap of target features with annotation features
An S4 class that information on overlap of target features with annotation features
Get distance to nearest TSS and gene id from AnnotationByGeneParts
Function that computes a max value
Function that computes a mean value
Function that computes a median value
Function that computes a min value
Ops method for a ScoreMatrix object. It enables to use arithmetic, indicator and logic operations on ScoreMatrix objects.
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.
An S4 class for storing 'getRandomEnrichment' function results
An S4 class for storing 'ScoreMatrix' function results
Get base-pair score for bases in each window
Get bin score for bins on each window
An S4 class for storing a set of 'ScoreMatrixList'
Make ScoreMatrixList from multiple targets
Function that computes a sum value
annotatGrWithGeneParts function
Function to annotate given GRanges object with a given genomic feature
Function to annotate a given GRanges object with promoter,exon,intron & intergenic values
Annotate given ranges with genomic features
Annotate given object with promoter, exon, intron and intergenic regions
bed12ToExons function
bed12ToIntrons function
Bins the columns of a matrix using a user provided function
Function that computes a maximum value for each bin
Function that computes a mean value for each bin
Function that computes a median value for each bin
Function that computes a minimum value for each bin
Function that computes a sum of values in a bin
binner function
c.ScoreMatrix
c.ScoreMatrixList
Example CAGE data set.
function that calculates the significance of overlaps of two sets of features using randomization
checkBedValidity function
checkClass function
compressedAndUrl2temp function
constrainRanges function
convert a data frame read-in from a bed file to a GRanges object for exons
convert a data frame read-in from a bed file to a GRanges object for introns
convert a data frame read-in from a bed file to a GRanges object
Example CpG island data set.
detectUCSCheader function
distance2NearestFeature function
Compute an enrichment of IP over control both stored in ScoreMatrix objects
Compute an enrichment of IP (stored in ScoreMatrixList object) over control (stored in ScoreMatrix object)
Compute an enrichment of IP over control both stored in ScoreMatrixList objects
file.ext function
Find combitations of genomic features
galpTo2Ranges function
Example RefSeq genes data set.
getColors function
Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature
Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands
Get the membership slot of AnnotationByFeature
get enrichment based on randomized feature overlap
Get the percentage of target features overlapping with annotation from AnnotationByFeature
Converts a gff formated data.frame into a GenomicRanges object.  The GenomicRanges object needs to be properly formated for the function to work.
Draw a heatmap of a given ScoreMatrix object
Heatmap for meta-region profiles
Plots the percentage of overlapping intervals with genomic features in a heatmap
Get common rows from all matrices in a ScoreMatrixList object
Function creates a matrix storing data with desirable number of bins for each window
Function creates a matrix storing data with desirable number of bins for each window
Function creates a matrix storing data with desirable number of bins for each window
Function creates a matrix storing data with desirable number of bins for each window
Function creates a matrix storing data with desirable number of bins for each window
Draw multiple heatmaps from a ScoreMatrixList object
Reorder all elements of a ScoreMatrixList to a given ordering vector
Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window
Line plot(s) for meta-region profiles
Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature
Example promoter data set.
function that randomizes the genomic coordinates
read.zip function
readBam function
Read a BED file and convert it to GRanges.
readBigWig function
A function to read the Encode formatted broad peak file into a GRanges object
A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores
Read a tabular file and convert it to GRanges.
A function to read the Encode formatted narrowPeak file into a GRanges object
readTableFast function
Function for reading exon intron and promoter structure from a given bed file
Scales the values in the matrix by rows and/or columns
Scale the ScoreMatrixList
show method for some of the genomation classes
Extract method for a ScoreMatrix object.
Extract method for a ScoreMatrixList object.
target.type function