如何使用 proxy::dist 应用自定义函数来在 R 中创建距离矩阵

Question

我定义了一个自定义函数并测试了该函数以确保它有效，但我无法将其应用于列表以获得距离矩阵。

我的代码是：

library(Biostrings)
library(proxy)

#import the sequences using Biostrings
indf<-readAAStringSet("C:/Users/jamie/OneDrive/Documents/Junk/SAMPLEFASTA.fasta")

#Assign the names and sequences to different variables
seqAAname<-names(indf)
seqz<-paste(indf)

#Put just the sequences into a dataframe
indf2<-data.frame(seqz)

#Convert the sequences into a list
indf3<-as.list(indf2)

#Define a custom function to return the alignment score between two sequences (pairwise)
customalnfunc <- function(X, Y){
  pairwiseAlignment(X, Y,
                    substitutionMatrix = "BLOSUM45", gapOpening = 1, gapExtension = 3)
}

#Test the function but not as a function (This works fine)
testfreefunc<-  pairwiseAlignment(AAString("PEHQRSTVE"),AAString("PQHQRETVE"),
                    substitutionMatrix = "BLOSUM45", gapOpening = 1, gapExtension = 3)
print(testfreefunc@score)


#Test the function as a fucntion to make sure it works (This works fine)
testfuncout <- customalnfunc(AAString("PEHQRSTVE"),AAString("PQHQRETVE"))
print(testfuncout@score)

#Apply the custom function to all possible pairs using proxy::dist with the custom function (This does not work, it returns 0)
outalnmatrix <- proxy::dist(indf3, method = customalnfunc)
outalnmatrix

SAMPLEFASTA.fasta 文件包含：

>SeqA
PEHQRSTVE
>SeqB
PQHQRETVE
>SeqC
RQHERSEVE

outalnmatrix 所需的输出是：

我尝试将输入数据作为列表和矩阵传递给 proxy::dist 。

我怎样才能做到这一点？

Answer 1

您不需要使用 proxy 包，因为 proxy::dist 旨在对矩阵/数据帧的行进行相互比较。由于要比较字符串，因此可以使用outer。但是，您需要调整 customalnfunc 函数，以便它仅返回一个数字 (scoreOnly = TRUE)。

library(Biostrings)

seqz <- c("PEHQRSTVE", "PQHQRETVE", "RQHERSEVE")

customalnfunc <- function(X, Y){
  pairwiseAlignment(X, Y,
                    substitutionMatrix = "BLOSUM45",
                    gapOpening = 1,
                    gapExtension = 3,
                    scoreOnly = TRUE)
}

outer(seqz, seqz, customalnfunc)

#>
     [,1] [,2] [,3]
[1,]   58   50   33
[2,]   50   60   33
[3,]   33   33   57