CoreIntervals: Computing the Core Intervals for Both Classes.

In propOverlap: Feature (gene) selection based on the Proportional Overlapping Scores

Description

CI.emprical is used to compute the core interval boundaries for each class.

Usage

CI.emprical(ES, Y)

Arguments

ES	gene (feature) matrix: P, number of genes, by N, number of samples(observations).
Y	a vector of length N for samples' class label.

Value

CI.emprical returns an object of class “data.frame” which has P rows and 4 columns. The first two columns represent a1, the minimum boundary of the first class, and b1, the maximum boundary of the first class, respectively. Whereas, the last two columns represent a2, the minimum boundary of the second class, and b2, the maximum boundary of the second class, respectively.

Author(s)

Osama Mahmoud [e-mail]

References

Mahmoud O., Harrison A., Perperoglou A., Gul A., Khan Z., Metodiev M. and Lausen B. (2014) A feature selection method for classification within functional genomics experiments based on the proportional overlapping score. BMC Bioinformatics, 2014, 15:274.

Examples

data(lung)
GenesExpression <- lung[1:12533,]   #define the features matrix
Class           <- lung[12534,]     #define the observations' class labels
CoreIntervals   <- CI.emprical(GenesExpression, Class)
CoreIntervals[1:10,]                #show classes' core interval for the first 10 features

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

        X1      X2       X3      X4
1    47.75  449.75   -59.20  470.40
2     0.05   89.25   -43.20  126.40
3   -48.25   56.15   -47.70   75.50
4  -318.85   30.35  -239.15  218.05
5   -35.25   85.15   -43.10   44.90
6  -737.40 1958.60  -516.95 1795.45
7   -56.05  101.95   -47.10   64.10
8    15.20 1100.00  -113.50  995.30
9  -567.30 1899.90 -2040.10 4629.50
10 -189.85 1884.15   378.30 1496.70

propOverlap documentation built on May 1, 2019, 10:55 p.m.