MEDIPSset-class: MEDIPSset class and internal functions
In paolopavan/medips: DNA IP-seq data analysis

Description Objects from the Class Slots Methods Author(s) Examples

MEDIPSset class is used in the MEDIPS library in order to store and extract objects and information from the input file as well as parameter settings specified during the workflow.

Objects of the classes contain information about the provided short reads, MeDIP raw/count signals, and further parameter settings. A MEDIPS SET object is created by the MEDIPS.genomeVector() function. According slots will be filled during the workflow.

genome_name:: Object of class "character" : the refernce genome
window_size:: Object of class "numeric" : the window size for the genome vector
chr_names:: Object of class "character" : the names of the chromosomes included within the MEDIPS/COUPLING SET
chr_lengths:: Object of class "numeric" : the lengths of the chromosomes included within the MEDIPS/COUPLING SET
sample_name:: Object of class "character" : the name of the input file
path_name:: Object of class "character" : the path to the input file
number_regions:: Object of class "numeric" : the total number of included regions
genome_count:: Object of class "numeric" : the raw MeDIP-seq signals at the genomic bins
extend:: Object of class "numeric" : the length of the regions after extension
shifted:: Object of class "numeric" : the number of bases by which the reads are shifted along the sequencing direction
uniq:: Object of class "logical" : determines if all reads mapping to exactly the same genomic position should be kept (uniq = 0), replaced by only one representative (uniq = 1), or if the number of stacked reads should be capped by a maximal number of stacked reads per genomic position determined by a poisson distribution of stacked reads genome wide and by a given p-value (1 > uniq > 0).

genome_name: signature(object = "MEDIPSset"): extracts the reference genome of the MEDIPS SET
window_size: signature(object = "MEDIPSset"): extracts the window size from the bin_size slot of the MEDIPS SET
chr_names: signature(object = "MEDIPSset"): extracts the names of the chromosomes included within the MEDIPS SET
chr_lengths: signature(object = "MEDIPSset"): extracts the length of the chromosomes included within the MEDIPS SET
fragmentLength: signature(object = "MEDIPSset"): extracts the estimated fragment length of the DNA fragments
sample_name: signature(object = "MEDIPSset"): extracts the name of the input file
path_name: signature(object = "MEDIPSset"): extracts the path to the input file
number_regions: signature(object = "MEDIPSset"): extracts the total number of included regions
genome_count: signature(object = "MEDIPSset"): extracts the raw MeDIP-Seq signals at the genomic bins
extend: signature(object = "MEDIPSset"): extracts the number of bases by which the regions are extended
show: signature(object = "MEDIPSset"): prints a summary of the MEDIPS SET object content
shifted: signature(object = "MEDIPSset"): extracts the number of bases by which the regions are shifted
uniq: signature(object = "MEDIPSset"): extracts the specified value for the uniq parameter
MEDIPS.GenomicCoordinates: signature(object = "MEDIPSset"): internal function for calculating coordinates for the genomic bins
MEDIPS.readRegionsFile: signature(object = "MEDIPSset"): internal function for reading short read information
MEDIPS.calibrationCurve: signature(object = "MEDIPSset"): internal function for calculating the calibration curve
MEDIPS.cnv: signature(object = "MEDIPSset"): internal function for calculating CNVs in case two groups of INPUT SETs have been provided to the MEDIPS.meth function
MEDIPS.diffMeth: signature(object = "MEDIPSset"): internal function for calculating differential coverage in case two groups of MEDIPS SETs have been provided to the MEDIPS.meth function
MEDIPS.getPositions: signature(object = "MEDIPSset"): internal function for receiving genomic coordinates of a given sequence pattern (e.g. CG)
MEDIPS.rms: signature(object = "MEDIPSset"): internal function for calculating relative methylation scores
matNnotNA: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matMin: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matDiff: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matMax: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matMean: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matSd: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test
matTtest: signature(object = "MEDIPSset"): internal function for vectorized calculation of the t.test