Description Usage Arguments Details Value Author(s) References See Also Examples
POS
computes the proportional overlapping scores of the given genes (features). This score measures the overlap degree between gene expression values across various classes. It produces a value lies in the interval [0,1]. A lower score denotes gene with higher discriminative power for the considered classification problem.
1 | POS(ES, Core, Y)
|
ES |
gene (feature) matrix: P, number of genes, by N, number of samples(observations). |
Core |
a |
Y |
a vector of length N for samples' class label. |
For each gene, POS
computes a measure that estimates the overlapping degree between the expression intervals of different classes. For estimating the overlap, POS measure takes into account three factors: the length of the overlapping region; number of the overlapped samples (observations); the proportion of each class's overlapped samples to the total number of overlapping samples.
It returns a vector of length P for ‘POS’ measures of all genes (features).
Osama Mahmoud ofamah@essex.ac.uk
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.
CI.emprical
for the core interval boundaries and GMask
for the gene masks.
1 2 3 4 5 |
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gene 1 gene 2 gene 3 gene 4 gene 5
0.6616993 0.5150381 0.4701053 0.4552750 0.1483130
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0000 0.1698 0.3510 0.3537 0.5404 0.8668
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