RankedGeneList-class: Class RankedGeneList

In palenic/genePrioritization: Find Potential Disease-Related Genes

Description

A S4 class to store results of a genePrioritization analysis.

Slots

results

A named vactor of candidate scores sorted according to increasing score

seed

The seed genes

candidates

The candidate genes sorted according to increasing score

coexpr

A named matrix of shape (nCandidates, nSeed) with coexpression values between each seed and each candidate. Rows are sorted according to increasing candidate score.

ranks

A named matrix of shape (nCandidates, nSeed) with ranks of each candidate in each seed gene coexpression list. Candidates are ranked according to their decreasing coexpression. Rows are sorted according to increasing candidate score

See Also

prioritizeCandidates

Examples

a <- matrix(c(1,2,3,2,4,6,8,6,4,5,2,8,7,1,5),
nrow=5, ncol=3,byrow=TRUE)
colnames(a) <- c('sample1','sample2','sample3')
rownames(a) <- c('gene1','gene2','gene3','gene4','gene5')
seed <- c('gene1')
candidates <- c('gene2','gene4')
x <- findCoexpression(counts=a, seedGenes=seed)
y <- rankGenes(x)
z <- candidateScoring(y, candidates)
result <- RankedGeneList(seed=seed, candidates=candidates,
                        results=z,
                        coexpr=x[candidates,,drop=FALSE],
                        ranks=y[candidates,,drop=FALSE])

palenic/genePrioritization documentation built on Sept. 13, 2020, 12:16 a.m.