MEDIPSset class and internal functions

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Description

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 from the Class

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.

Slots

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).

Methods

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

Author(s)

Lukas Chavez, Joern Dietrich

Examples

1
showClass("MEDIPSset")

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