Knet: Measure the strength of association between a phenotype and a...

In SANTA: Spatial Analysis of Network Associations

Description

Compute the strength of clustering of high-weight vertices (hits) on a network using a modified version of Ripley's K-statistic. This method can be used to measure the strength of association between a phenotype or function and a network.

Usage

Knet(g, nperm=100, dist.method=c("shortest.paths", "diffusion", "mfpt"),
vertex.attr="pheno", edge.attr=NULL, correct.factor=1, nsteps=1000, 
prob=c(0, 0.05, 0.5, 0.95, 1), parallel=NULL, B=NULL, verbose=TRUE)

Arguments

g	igraph object, the network to work on.
nperm	Integer value, the number of permutations to be completed.
dist.method	String, the method used to calculate the distance between vertex pairs.
vertex.attr	Character vector, the name of the vertex attributes under which the vertex weights to be tested are stored. The vector can contain one or more elements.
edge.attr	String, the name of the edge attribute to be used as distances along the edges. If an edge attribute with this name is not found, then each edge is assumed to have a distance of 1.
correct.factor	Numeric value, if the network contains unconnected vertices, then the distance between these vertices is set as the maximum distance between the connected vertices multiplied by correct.factor.
nsteps	Integer value, the number of bins into which vertex pairs are placed.
prob	Numeric vector, the quantiles to be calculated for the Knet permutations.
parallel	Numeric value or NULL. If parallel computing is available, this value denotes the number of cores that the computation will be split over.
B	Symmetrical numeric matrix. A precomputed distance bin matrix for g output by the BinGraph function. If NULL, then B is computed within the Knet function.
verbose	Logical, if TRUE messages about the progress of the function are displayed.

Details

The SANTA method uses the 'guilt-by-association' principle to measure the strength of association between a network and a phenotype. It does this by measuring the strength of clustering of the phenotype scores across the network. The stronger the clustering, the greater the association between the network and the phenotype.

The SANTA method applies Ripley's K-function, a well-established approach to spatial statistics that measures the strength of clustering of points on a plane, and extends it in a number of ways. First, a Knet function is defined by adapting the approach for networks using vertex pair distance measures. Second, vertex weights are incorporated into Knet and the importance of vertices made relative to their own associated weight. Third, the mean vertex weight is subtracted from each individual vertex weight when calculating the Knet function. This means that the Knet function measures the degree of vertex weight clustering relative to a random distribution of vertex weights. The Knet function is defined as

K^{net}[s] = 2/p^2 * sum_i{(p_i) sum_j{(pj - bar{p}) I(dg(i,j)<=s)}}

where p_i is the weight of vertex i, \bar{p} is the mean vertex weight across all vertices, and I(dg[i,j]<=s) is an identity function, equaling 1 if vertex i and vertex j are within distance s and 0 otherwise.

In order to derive a p-value and quantify the significance of the observed distribution of weights, the observed Knet-curve is compared to Knet-curves obtained using the same network but randomly permuted vertex weights. Vertices with missing weights (NA) are not included within these permutations. The area under the Knet-curve (AUK) is calculated for the observed network and each of the permuted networks and a z-score used to produce a p-value. This p-value indicates the probability an observed AUK at least this high is seen given the null hypothesis that the vertex weights are randomly distributed.

If parallel computing is possible, parallel can be used to split permutations over multiple cores. The snow package is used to manage the parallel computing. If parallel=NULL or parallel computing is not possible, then only one core is used. If a positive integer is input and parallel computing is possible, then the permutations are split over up to this many cores.

Vertex weights should be greater or equal that zero or equal to NA if the weight is missing.

Value

If one vertex attribute is input, Knet is run on the single set of vertex weights and a list containing the statistics below is returned. If more than one vertex attribute is input, then Knet is run on each set of vertex weights and a list containing an element for each vertex attribute is returned. Each element contains a sub-list containing the statistics below for the relevant vertex attribute.

K.obs	Knet-function curve for the observed vertex weights.
AUK.obs	Area under the Knet-function curve (AUK) for the observed vertex weights.
K.perm	Knet-function curve for each permutation of vertex weights. Equals NA if no permutations are completed.
AUK.perm	Area under the Knet-function curve (AUK) for each permutation of vertex weights. NA if no permutations are completed.
K.quan	Quantiles for the permuted Knet-function curves. NA if no permutations are completed.
pval	p-value, calculated from a z-score derived from the observed and permuted AUKs. NA if no permutations are completed.

Author(s)

Alex J. Cornish [e-mail] and Florian Markowetz

References

Cornish, A.J. and Markowetz, F. (2014) SANTA: Quantifying the Functional Content of Molecular Networks.. PLOS Computational Biology. 10:9, e1003808.

Okabe, A. and Yamada, I. (2001). The K-function method on a network and its computational implementation Geographical Analysis. 33(3): 271-290.

See Also

Knode

Examples

# apply Knet to a network with hit clustering
g.clustered <- barabasi.game(50, directed=FALSE)
g.clustered <- SpreadHits(g.clustered, h=10, lambda=10)
res.clustered <- Knet(g.clustered, nperm=100, vertex.attr="hits")
res.clustered$pval
plot(res.clustered)

# apply Knet to a network without hit clustering
g.unclustered <- barabasi.game(50, directed=FALSE)
g.unclustered <- SpreadHits(g.unclustered, h=10, lambda=0)
res.unclustered <- Knet(g.unclustered, nperm=100, vertex.attr="hits")
res.unclustered$pval
plot(res.unclustered)

Example output

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

computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance bins... done
computing the clustering of the 'hits' weights using 100 permutations...  done
[1] 9.935866e-06
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance bins... done
computing the clustering of the 'hits' weights using 100 permutations...  done
[1] 0.720808

SANTA documentation built on Oct. 31, 2019, 3:21 a.m.