CosineDFV: calculate disease similarity by using feature vectors

Description Usage Arguments Value Author(s) References Examples

View source: R/CosineDFV.R

Description

given two (lists of) disease names, this function will calculate cosine similarity between these diseases' feature vectors.

Usage

1
CosineDFV(D1, D2, d2f, dcol = 2, fcol = 1, ccol = 3)

Arguments

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

Value

a matrix of disease disease similarity which rownames and colnames are the disease names

Author(s)

Zhihui Fei, Peng Ni, Min Li

References

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.

Examples

1
2
3
4
5
### 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)

dSimer documentation built on Nov. 17, 2017, 12:51 p.m.