CosineDFV {dSimer} | R Documentation |
given two (lists of) disease names, this function will calculate cosine similarity between these diseases' feature vectors.
CosineDFV(D1, D2, d2f, dcol = 2, fcol = 1, ccol = 3)
D1 |
a vector consists of disease ids/names |
D2 |
another vector consists of disease ids/names |
d2f |
data.frame, contains term co-occurrences between features and diseases |
dcol |
integer, disease column number in d2f |
fcol |
integer, feature column number in d2f |
ccol |
integer, co-occurrences column number in d2f |
a matrix of disease disease similarity which rownames and colnames are the disease names
Zhihui Fei, Peng Ni, Min Li
Zhou X Z, Menche J, Barabasi A L, et al. Human symptoms-disease network[J]. Nature communications, 2014, 5.
Van Driel M A, Bruggeman J, Vriend G, et al. A text-mining analysis of the human phenome[J]. European journal of human genetics, 2006, 14(5): 535-542.
### this is a disease-symptom-cooccurrence sample, if you want to use ### the complete data, please use "data(d2s_hsdn)" command data(d2s_hsdn_sample) ds <- sample(unique(d2s_hsdn_sample[,2]), 10) simmat <- CosineDFV(ds, ds, d2s_hsdn_sample)