计算塔莫托系数

Question

我想计算疾病pairs.The样本数据以下的Tanimoto系数(集合/Union的交集)，只对一个疾病对计算。疾病1为NK细胞缺陷，2为腺苷丁二酸裂解酶缺乏。

Set 1是疾病1 (NK细胞缺陷)，它包含来自Gene1柱的所有基因。

Set 2为疾病2(Adenylo琥珀酸裂解酶缺乏症)，它含有来自Gene2柱的所有基因。

**Gene1** **Gene2**  **Disease1**   **Disease2**
IMPDH1  XDH NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  ADA NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  NPR1    NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  IMPDH1  NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  IMPDH2  NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  PPP3R2  NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  RRM1    NK cell defects Adenylosuccinate lyase deficiency
NPR1    POLA1   NK cell defects Adenylosuccinate lyase deficiency
PPP3R2  ITGAL   NK cell defects Adenylosuccinate lyase deficiency
ITGAL   NPR1    NK cell defects Adenylosuccinate lyase deficiency
CASP3   NPR1    NK cell defects Adenylosuccinate lyase deficiency
PTK2B   NPR1    NK cell defects Adenylosuccinate lyase deficiency
TNF GUCY1A2 NK cell defects Adenylosuccinate lyase deficiency
PTK2B   GUCY1A2 NK cell defects Adenylosuccinate lyase deficiency

对于如何在MySQL或R中这样做，有什么建议吗？

谢谢,

罗汉

Answer 1

随机输入数据-

library(data.table)

DT = data.table(
  G1=1:5,
  G2=3:7,
  D1="A",
  D2="B"
  )

DT[,
   list(
     intersectG = length(intersect(G1,G2)),
     unionG = length(union(G1,G2)),
     Tanimoto = length(union(G1,G2))/length(intersect(G1,G2))
     ),
   by = c('D1','D2')]

产出-

   D1 D2 intersectG unionG Tanimoto
1:  A  B          3      7 2.333333

Answer 2

学会搜索：

 install.packages("sos")
 library("sos")
 findFn("Tanimoto")

getGeneSim {GOSim} R文档

计算基因的功能相似性

描述

计算使用不同策略的基因列表的成对功能相似点。用法

getGeneSim(genelist1, genelist2=NULL, similarity="funSimMax", similarityTerm="relevance", 
           normalization="Tanimoto", method="sqrt", avg=(similarity=="OA"), verbose=FALSE)