Description Usage Arguments Value Note Author(s) References See Also Examples
Function SNFb
performs SNF but first determines the subsets
of neighbours and then normalization is performed on the neighbours only.
The function is based on the functions affinityMatrix
and snf
from the SNFtool package.
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List |
A list of matrices of the same type. It is assumed the rows are corresponding with the objects. |
type |
Type indicates whether the provided matrices in "List" are either data matrices, distance matrices or clustering results obtained from the data. If type="dist" the calculation of the distance matrices is skipped and if type="clusters" the single source clustering is skipped. Type should be one of "data", "dist" or"clusters". |
distmeasure |
A vector of the distance measures to be used on each data matrix. Should be of "tanimoto", "euclidean", "jaccard","hamming". |
method |
A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names. |
normalize |
Logical. Indicates whether to normalize the distance matrices or not.
This is recommended if different distance types are used. More details
on standardization in |
NN |
The number of neighbours to be used in the procedure. |
mu |
The parameter epsilon. The value is recommended to be between 0.3 and 0.8. |
T |
The number of iterations. |
clust |
Choice of clustering function (character). Defaults to "agnes". |
linkage |
Choice of inter group dissimilarity (character). Defaults to "ward". |
alpha |
The parameter alpha to be used in the "flexible" linkage of the agnes function. Defaults to 0.625 and is only used if the linkage is set to "flexible" |
StopRange |
Logical. Indicates whether the distance matrices with values not between zero and one should be standardized to have so.
If FALSE the range normalization is performed. See |
The returned value is a list with two elements:
FusedM |
The fused similarity matrix |
DistM |
The distance matrix computed by subtracting FusedM from one |
Clust |
The resulting clustering |
For now, only hierarchical clustering with the agnes
function link is implemented.
Marijke Van Moerbeke
WANG, B., MEZLINI, M. A., DEMIR, F., FIUME, M., TU, Z., BRUDNO, M., HAIBE-KAINS, B., GOLDENBERG, A. (2014). Similarity Network Fusion for aggregating data types on a genomic scale. Nature. 11(3) pp. 333-337. WANG, B., MEZLINI, M. A., DEMIR, F., FIUME, M., TU, Z., BRUDNO, M., HAIBE-KAINS, B., GOLDENBERG, A. (2014). SNFtool: Similarity Network Fusion. R package version 2.2
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