qseaSet-class: qseaSet class and its methods

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

qseaSet class and its methods

Description

The qseaSet class is used in qsea to store information about the coverage, the dependent organism, the chromosomes included in the input file, the length of the included chromosomes (automatically loaded), the number of regions, and optionally CNV information.

Slots

sampleTable:

Object of class "data.frame": the sample table

count_matrix:

Object of class "matrix": matrix containing the coverage for all samples

zygosity:

Object of class "matrix": matrix containing the zygosity for all chromosomes and all samples

regions:

Object of class "GenomicRanges": the genomic regions for the coverage matrix

parameters:

Object of class "list": the parameter list used to create this object

cnv:

Object of class "GenomicRanges": CNV ranges and logFCs

enrichment :

Object of class "list": parameters of the sequence pattern enrichment analysis

libraries :

Object of class "matrix": parameters of the sequencing libraries

Methods

getSampleTable

signature(object = "qseaSet"): extracts the sample table of a qsea set

getSampleNames

signature(object = "qseaSet"): extracts the sample names of a qsea set

getSampleGroups

signature(object = "qseaSet"): extracts the sample groups of a qsea set

getChrNames

signature(object = "qseaSet"): returns the analysed chromosomes

getCounts

signature(object = "qseaSet"): extracts the count matrix a qsea set

getRegions

signature(object = "qseaSet"): extracts the regions object of a qsea set

getParameters

signature(object = "qseaSet"): extracts the parameter list of a qsea set

getLibSize

signature(object = "qseaSet"): extracts the library size (eg the total number of read counts per sample)

getNormFactors

signature(object = "qseaSet"): extracts the list with the different normalization factors

hasCNV

signature(object = "qseaSet"): TRUE if CNV information is present, FALSE otherwise

getCNV

signature(object = "qseaSet"): extracts the CNV regions and logFCs

getOffset

signature(object = "qseaSet"): extracts offset of rpkm scaled background reads

getWindowSize

signature(object = "qseaSet"): returns the window size of the object

getZyosity

signature(object = "qseaSet"): returns the zygosity matrix of the object

setZygosity

signature(object = "qseaSet", zygosityMatrix): sets the zygosity matrix, and resets CNV

Author(s)

Matthias Lienhard

Examples

showClass("qseaSet")

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.