Question

我最近开始研究单倍型数据，而且我正在搞乱来自1000个基因组项目的数据，并试图用R中的Pegas包来操纵它。到目前为止我来了到目前为止：

library(pegas)
a <- "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502"
b <- "ALL.chrY.phase3_integrated_v1b.20130502.genotypes.vcf.gz"
url <- paste(a, b, sep = "/")
download.file(url, "chrY.vcf.gz")
(info <- VCFloci("chrY.vcf.gz"))
SNP <- is.snp(info)
X.SNP <- read.vcf("chrY.vcf.gz", which.loci = which(SNP))
h <- haplotype(X.SNP, 6020:6030)
net <- haploNet(h)
plot(net)

我想绘制一个单倍型网，但它并没有执行它。我收到以下消息：＆＃39; h＆＃39;必须是班级＆＃39;单倍型＆＃39;

如果我打印出来，我会得到：

> h
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19]
. "C"  "C"  "C"  "C"  "C"  "C"  "C"  "C"  "C"  "C"   "C"   "C"   "C"   "C"   "C"   "C"   "T"   "C"   "C"  
. "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"   "G"   "G"   "G"   "G"   "G"   "G"   "G"   "A"   "G"  
. "C"  "C"  "C"  "C"  "C"  "C"  "T"  "C"  "C"  "C"   "C"   "C"   "C"   "C"   "C"   "C"   "C"   "C"   "C"  
. "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"   "C"   "T"   "T"   "T"   "T"   "T"   "T"   "T"   "T"  
. "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"  "G"   "G"   "G"   "G"   "A"   "G"   "G"   "G"   "G"   "G"  
. "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"   "T"   "C"   "T"   "T"   "T"   "T"   "T"   "T"   "T"  
. "A"  "A"  "A"  "A"  "A"  "A"  "A"  "A"  "A"  "C"   "A"   "A"   "A"   "A"   "A"   "A"   "A"   "A"   "A"  
. "G"  "G"  "G"  "."  "G"  "G"  "G"  "G"  "G"  "G"   "G"   "G"   "A"   "G"   "G"   "G"   "G"   "G"   "G"  
. "."  "T"  "C"  "T"  "T"  "C"  "T"  "."  "."  "."   "T"   "T"   "T"   "T"   "C"   "T"   "T"   "T"   "T"  
. "."  "A"  "."  "A"  "."  "C"  "A"  "A"  "C"  "."   "A"   "A"   "A"   "A"   "A"   "C"   "A"   "A"   "A"  
. "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"  "T"   "T"   "T"   "T"   "T"   "T"   "T"   "T"   "T"   "C"  
attr(,"class")
[1] "haplotype.loci"
attr(,"freq")
 [1]   18 1142    2    5   25    6    1    4    2    1    2    5    1    9    1    3    1    4    1

它显然分配了19个单倍型。数据的呈现方式必定存在问题。有什么建议？此外，Pegas上的材料非常少，以及如何使用Pegas操作VCF文件。有没有人知道一个很好的资源（网页或书籍）来获取有关如何使用VCF文件中的单倍型进行操作的信息，它甚至不必为Pegas，任何R库都可以，或者Python ...任何事情真。

谢谢你的帮助，彼得

Answer 1

我知道这是一篇旧帖子，但是如果其他人出现同样的问题，我已经找到了解决问题的方法。使用pacakage“vcfR”您可以使用read.vcfR（）读取vcf，然后使用vcfR2DNAbin（）将其转换为DNAbin。在DNAbin上使用单倍型（）导致一类“单倍型”而非“单倍型。自我”。

Answer 2

这是预期的结果：目前，haploNet（）仅适用于由DNA seqs（“DNAbin”类）产生的“单倍型”类。 read.vcf（）的输出是“loci”类，haplotype（）是两个类的泛型函数。

如果您只处理SNP，可以通过以下方式避免这种情况：

class(h) <- NULL
h <- as.DNAbin(h)

（终极）目标是让haploNet（）也与“haplotype.loci”（仍在开发中）和其他人一起工作。

干杯，艾曼纽尔

R :( Pegas）单倍型问题 - （错误：＆＃39; h＆＃39;必须是类＆＃39;单倍型＆＃39;）

2 个答案: