我試圖使用snpStats包執行關聯。我有一個名爲'plink'的snp矩陣,其中包含我的基因型數據(如 $基因型列表,$ map,$ fam),並且plink $ genotype具有:SNP名稱作爲列名稱(2個SNP)和主題標識符作爲行名稱:循環遍歷R中的S4對象中的列
plink$genotype
SnpMatrix with 6 rows and 2 columns
Row names: 1 ... 6
Col names: 203 204
的砰砰數據集可以再現複製下面的PED和映射文件並將其保存爲「plink.ped」分別plink.map」:
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
然後以這種方式使用plink:
./plink --file plink --make-bed
@[email protected]
| 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/ |
@[email protected]
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
我也有一個包含結果的表型數據幀(outcome1,outcome2,...)我想與基因型,這是該關聯:
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)
協會工程當我做的唯一條件是:(用公式「snp.rhs.test」):
bmi<-snp.rhs.tests(bmi~sex+age,family="gaussian", data=pheno, snp.data=plink$genotype)
我的問題是,我怎麼通過成果循環?這種類型的數據 似乎不同於其他所有人,我在操作它時遇到問題 ,所以如果您有一些教程的建議 可以幫助我瞭解如何執行此操作以及其他操作(如子集),我也將不勝感激。例如,snp.matrix數據。
這是我曾嘗試循環:
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
然後我嘗試這樣的:
for (cov in names(pheno)) {
association<-snp.rhs.tests(cov, family="gaussian",data=pheno, snp.data=plink$genotype)
}
Error in eval(expr, envir, enclos) : object 'bmi' not found
感謝您像往常一樣對你的幫助! -f
你有沒有我們玩的例子數據集? –
你不能在矩陣上使用'$',而是使用'snp.matrix [,'genotype']'代替 – James
對不起,我厭倦了讓我的問題更清楚,我會嘗試添加生成的snpmatrix數據plink如果仍然令人困惑... – user971102