# MEDIPSset class and internal functions

### 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")
``` |