我正在尝试使用snpStats包执行关联。
我有一个名为“plink”的 snp 矩阵，其中包含我的基因型数据（作为 $genotypes、$map、$fam 的列表），并且 plink$genotype 具有：SNP 名称作为列名（2 个 SNP）和主题标识符作为行名：
plink$genotype
SnpMatrix with 6 rows and 2 columns
Row names: 1 ... 6
Col names: 203 204
可以复制以下 ped 和 map 文件并分别将它们保存为“plink.ped”和 plink.map 来复制 plink 数据集：
plink.ped:
1 1 0 0 1 -9 A A G G
2 2 0 0 2 -9 G A G G
3 3 0 0 1 -9 A A G G
4 4 0 0 1 -9 A A G G
5 5 0 0 1 -9 A A G G
6 6 0 0 2 -9 G A G G
plink.map:
1 203 0 792429
2 204 0 819185
然后以这种方式使用plink：
./plink --file plink --make-bed
@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Web-based version check ( --noweb to skip )
Recent cached web-check found...Problem connecting to web
Writing this text to log file [ plink.log ]
Analysis started: Tue Nov 29 18:08:18 2011
Options in effect:
--file /ugi/home/claudiagiambartolomei/Desktop/plink
--make-bed
2 (of 2) markers to be included from [ /ugi/home/claudiagiambartolomei/Desktop /plink.map ]
6 individuals read from [ /ugi/home/claudiagiambartolomei/Desktop/plink.ped ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 6 missing
4 males, 2 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 2 SNPs
6 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 2 SNPs
After filtering, 0 cases, 0 controls and 6 missing
After filtering, 4 males, 2 females, and 0 of unspecified sex
Writing pedigree information to [ plink.fam ]
Writing map (extended format) information to [ plink.bim ]
Writing genotype bitfile to [ plink.bed ]
Using (default) SNP-major mode
Analysis finished: Tue Nov 29 18:08:18 2011
我还有一个表型数据框，其中包含我想与基因型关联的结果（结果 1、结果 2、...），即：
ID<- 1:6
sex<- rep(1,6)
age<- c(59,60,54,48,46,50)
bmi<- c(26,28,22,20,23, NA)
ldl<- c(5, 3, 5, 4, 2, NA)
pheno<- data.frame(ID,sex,age,bmi,ldl)
当我这样做时，该关联适用于单个术语：（使用公式“snp.rhs.test”）：
bmi<-snp.rhs.tests(bmi~sex+age,family="gaussian", data=pheno, snp.data=plink$genotype)
我的问题是，我如何遍历结果？这种类型的数据似乎与所有其他类型的数据不同，我在操作它时遇到了麻烦，所以如果您有一些教程的建议可以帮助我理解如何执行此操作和其他操作（例如子集 snp.matrix），我将不胜感激以数据为例。
这是我为循环尝试过的：
rhs <- function(x) {
x<- snp.rhs.tests(x, family="gaussian", data=pheno,
snp.data=plink$genotype)
}
res_ <- apply(pheno,2,rhs)
Error in x$terms : $ operator is invalid for atomic vectors
然后我尝试了这个：
for (cov in names(pheno)) {
association<-snp.rhs.tests(cov, family="gaussian",data=pheno, snp.data=plink$genotype)
}
Error in eval(expr, envir, enclos) : object 'bmi' not found
像往常一样感谢您的帮助！-F