StatisticsForPREDA-class: Class "StatisticsForPREDA" is used to manage the datamatrix...

In PREDA: Position Related Data Analysis

Description

This class is used to manage the datamatrix containing statistics for PREDA analyses: i.e. the gene (or other genomic feature) centered statistics accounting for differential expression (or for the other type of variation under investigation)

Objects from the Class

Objects can be created by calls of the form new("StatisticsForPREDA", ids, statistic, analysesNames, testedTail).

Slots

ids:

Object of class "character" a character vector of unique identifiers for the genomic features under investigation

statistic:

Object of class "matrix" a numeric matrix containing gene-centered statistics (or statistics on genomic data centered on other genomic features under investigation). The statistics must be provided as a matrix of numeric values, with a number of rows equal to the length of "ids" slot and a number of columns equal to the length of "analysesNames" slot.

analysesNames:

Object of class "character" a character vector of unique names associated to each column of statistic matrix. This is just a name that will be used to identify each analysis.

testedTail:

Object of class "character" a character describing what tail of the statistic distribution will be analyzed during PREDA analysis. Possible values are "upper", "lower" or "both". Anyway we strongly recommend using PREDA analysis only for statistics on genomic data with a symmetric distribution around zero.

Methods

analysesNames

signature(.Object = "StatisticsForPREDA"): get the names of the analyses in the StatisticsForPREDA object

getStatisticByName

signature(.Object = "StatisticsForPREDA"): extract data for individual analyses using the analysis name

initialize

signature(.Object = "StatisticsForPREDA"): initialize method for StatisticsForPREDA objects

StatisticsForPREDA2dataframe

signature(.Object = "StatisticsForPREDA"): extract data as a dataframe with probeids as rownames

StatisticsForPREDAFilterColumns_neg

signature(.Object = "StatisticsForPREDA"): filter statistics to remove selected analyses

StatisticsForPREDAFilterColumns_pos

signature(.Object = "StatisticsForPREDA"): filter statistics to keep selected analyses

Note

This class is better described in the package vignette

Author(s)

Francesco Ferrari

See Also

"DataForPREDA", analysesNames,getStatisticByName StatisticsForPREDA2dataframe, StatisticsForPREDAFilterColumns_neg,StatisticsForPREDAFilterColumns_pos

Examples

showClass("StatisticsForPREDA")

PREDA documentation built on Nov. 8, 2020, 7:40 p.m.