mRMRe.Data-class: Class '"mRMRe.Data"'

Description Instantiation Mutual Information Matrix Slots Methods Author(s) See Also Examples

Description

mRMRe.Data is the class containing datasets. Most if not all of the routines in the mRMRe package use mRMRe.Data objects as primary input.

Such an object is instantiated with a data frame containing the sample sets and optionally, stratum, weight vectors and a prior matrix. In addition to basic accession functions, we describe several methods which serve to manipulate the contents of the dataset.

Note that mRMR.data function is a wrapper to easily create mRMRe.Data objects.

Instantiation

Objects are created via calls of the form new("mRMRe.Data", data, strata, weights, priors).

data: is expected to be a data frame with samples and features respectively organized as rows and columns. The columns have to be of type :numeric, ordered factor, Surv and respectively interpreted as :continuous, discrete and survival variables.

strata: is expected to be a vector of type :ordered factor with the strata associated to the samples provided in data.

weights: is expected to be a vector of type :numeric with the weights associated to the samples provided in data.

priors: is expected to be a matrix of type :numeric where priors[i, j]: denotes an forced association between features i and j in data. The latter takes into consideration the directionality of the relationship and must be a value between 0 and 1.

Mutual Information Matrix

The mim method computes and returns a mutual information matrix. A correlation between continuous features is estimated using an estimator specified in continuous_estimator; currently, :pearson, spearman, kendall, frequency are supported. The estimator for discrete features is Cramer's V and for all other combinations, concordance index.

When outX is set to TRUE, ties are ignored when computing the concordance index and otherwise, these are considered. The correlations are first computed per strata and these are then combined by the inverse variance weight mean of the estimates using a bootstrap_count number of bootstraps if the former parameter is greater than 0, and by the relative weights of each strata otherwise. The resulting correlation is then summated with the corresponding value in the priors matrix with the latter being weighed for a proportion prior_weight of a final, biased correlation.

Slots

sample_names:

Object of class "character" containing the sample names.

feature_names:

Object of class "character" containing the feature names.

feature_types:

Object of class "numeric" containing the internal representation of features/variables: 1 for numeric, 2 for ordered factor, and 3 for survival data

data:

Object of class "matrix" containing the internal representation of the data set.

strata:

Object of class "numeric" containing the feature strata.

weights:

Object of class "numeric" containing sample weights.

priors:

Object of class "matrix" containing the priors.

Methods

featureCount

signature(object = "mRMRe.Data"): Returns the number of features.

featureData

signature(object = "mRMRe.Data"): Returns a data frame corresponding to the data set.

featureNames

signature(object = "mRMRe.Data"): Returns a vector containing the feature names.

mim

signature(object = "mRMRe.Data", prior_weight = 0, continuous_estimator = c("pearson", "spearman", "kendall", "frequency"), outX = TRUE, bootstrap_count = 0): Computes and returns the mutual information matrix.

priors

signature(object = "mRMRe.Data"): Returns a matrix containing the priors.

priors<-

signature(object = "mRMRe.Data", value): Sets the prior matrix.

sampleCount

signature(object = "mRMRe.Data"): Returns the number of samples.

sampleNames

signature(object = "mRMRe.Data"): Returns a vector containing sample names.

sampleStrata

signature(object = "mRMRe.Data"): Returns a vector containing sample strata.

sampleStrata<-

signature(object = "mRMRe.Data", value): Sets the sample strata.

sampleWeights

signature(object = "mRMRe.Data"): Returns a vector containing sample weights.

sampleWeights<-

signature(object = "mRMRe.Data"): Sets the sample weights.

subsetData

signature(object = "mRMRe.Data", row_indices, column_indices): Returns another data object containing only the specified samples and features (rows and columns, respectively.)

Author(s)

Nicolas De Jay, Simon Papillon-Cavanagh, Benjamin Haibe-Kains

See Also

mRMRe.Filter-class, mRMRe.Network-class

Examples

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showClass("mRMRe.Data")

set.thread.count(2)

## load data
data(cgps)

## equivalent ways of building an mRMRe.Data object
ge <- mRMR.data(data = data.frame(cgps.ge[ , 1:10, drop=FALSE]))
ge <- new("mRMRe.Data", data = data.frame(cgps.ge[ , 1:10, drop=FALSE]))

## print data
print(featureData(ge)[1:3, 1:3])

## print feature names
print(featureNames(ge))

## print the first sample names
print(head(sampleNames(ge)))

## print the first sample weights
print(head(sampleWeights(ge)))

Example output

Loading required package: survival
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Class "mRMRe.Data" [package "mRMRe"]

Slots:
                                                                            
Name:   sample_names feature_names feature_types          data        strata
Class:     character     character       numeric        matrix       numeric
                                  
Name:        weights        priors
Class:       numeric        matrix
[1] 2
      geneid_3310 geneid_2978 geneid_6352
22RV1    4.714871    3.852822    4.367895
5637     4.349628    3.762097    4.400742
639_V    4.389094    3.744586    4.249098
 [1] "geneid_3310"  "geneid_2978"  "geneid_6352"  "geneid_2621"  "geneid_5337" 
 [6] "geneid_10594" "geneid_826"   "geneid_11224" "geneid_1982"  "geneid_8664" 
[1] "22RV1" "5637"  "639_V" "647_V" "697"   "769_P"
22RV1  5637 639_V 647_V   697 769_P 
    1     1     1     1     1     1 

mRMRe documentation built on Feb. 14, 2019, 5:08 p.m.