凑一凑热闹... kinship2基因遗传学[s:11]
library(kinship2)<br />
data(sample.ped)<br />
sample.ped[1:10,]</p>
<p>pedAll <- pedigree(id=sample.ped$id,<br />
dadid=sample.ped$father, momid=sample.ped$mother,<br />
sex=sample.ped$sex, famid=sample.ped$ped)<br />
print(pedAll)</p>
<p>ped1basic <- pedAll['1']<br />
ped2basic <- pedAll['2']<br />
print(ped1basic)<br />
print(ped2basic)<br />
plot(ped2basic)<br />
# plot(ped1basic)</p>
<p>kin2 <- kinship(ped2basic)<br />
kin2</p>
<p>pedAll <- pedigree(id=sample.ped$id,<br />
dadid=sample.ped$father, momid=sample.ped$mother,<br />
sex=sample.ped$sex, famid=sample.ped$ped)<br />
kinAll <- kinship(pedAll)<br />
kinAll[1:14,1:14]<br />
kinAll[40:43,40:43]<br />
kinAll[42:46, 42:46]</p>
<p>df2 <- sample.ped[sample.ped$ped==2,]<br />
names(df2)<br />
df2$censor <- c(1,1, rep(0, 12))<br />
ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, status=df2$censor)</p>
<p>ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, affected=df2$affected,<br />
status=df2$censor)<br />
aff2 <- data.frame(blue=df2$affected,<br />
bald=c(0,0,0,0,1,0,0,0,0,1,1,0,0,1))<br />
ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, affected=as.matrix(aff2),<br />
status=df2$censor)</p>
<p>df2 <- sample.ped[sample.ped$ped==2,]<br />
names(df2)</p>
<p>df2$censor <- c(1,1, rep(0, 12))<br />
ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, status=df2$censor)</p>
<p>ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, affected=df2$affected,<br />
status=df2$censor)<br />
aff2 <- data.frame(blue=df2$affected,<br />
bald=c(0,0,0,0,1,0,0,0,0,1,1,0,0,1))<br />
ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, affected=as.matrix(aff2),<br />
status=df2$censor)</p>
<p>## create twin relationships<br />
relate2 <- matrix(c(210,211,1,<br />
212,213,3), nrow=2, byrow=TRUE)<br />
ped2 <- pedigree(df2$id, df2$father, df2$mother,<br />
df2$sex, affected=as.matrix(aff2),<br />
status=df2$censor,<br />
relation=relate2)<br />
</p>