代替ヌクレオチドがミスセンス変異につながる場合

Question

私はSNPの有無にかかわらず大きな配列データを比較しようとしており、snpsを非同義語または同義語としてマークしています。私が言う必要が

ref[test$pos]=as.vector(test$ALT) 

、意志交換用リード：私はalternatriveものでrefferenceヌクレオチドを置き換えることができます

head(test) 

    pos ALT REF 
1 2 G T 
2 8 G T 
3 65 C G 
4 68 C G 
5 77 T C 
6 78 G C 

：.fastaシーケンスおよび保守（refference）とPLNIKから.bimファイルおよび代替ヌクレオチドを有しますアミノ酸の変化かどうか。私はseqinrパッケージを使用するつもりです、多分私は間違った方法ですか？ だから私は配列で2列、（altベクトルで代替ヌクレオチドは、高音域でマークされている）しました：私は、これはアミノ酸にベクトル変換することができ

ref=c("a","t","g","t","c","g","t","c","g","g","c","c","g","c","g","g","g","c", 
"c","a","a","g","a","c","a","a","c","g","g","a","g","a","t","a","c","c", 
"g","c","t","g","g","g","g","a","c","t","a","c","a","t","c","a","a","g", 
"t","g","g","a","t","g","t","g","c","g","g","c","g","c","c","g","g","t", 
"g","g","c","c","g","t","g","c","g","g","g","c","g","g","c","g","c","c", 
"a","t","g","g","c","c","a","a","c","c","t","c","c","a","g","c","g","c", 
"g","g","c","g","t","t","g","g","c","t","c","c","c","t","c","g","t","c", 
"c","g","t","g","a","c","a","t","t","g","g","c","g","a","c","c","c","c", 
"t","g","c","c","t","c","a","a","c","c","c","a","t","c","c","c","c","c", 
"g","t","t","a","a","g") 

alt=c("a","G","g","t","c","g","t","G","g","g","c","c","g","c","g","g","g","c", 
"c","a","a","g","a","c","a","a","c","g","g","a","g","a","t","a","c","c", 
"g","c","t","g","g","g","g","a","c","t","a","c","a","t","c","a","a","g", 
"t","g","g","a","t","g","t","g","c","g","C","c","g","C","c","g","g","t", 
"g","g","c","c","T","G","g","c","g","g","C","c","g","g","c","g","c","c", 
"a","t","g","g","c","c","a","a","c","c","t","c","c","a","g","c","g","c", 
"g","g","c","g","t","t","g","g","c","t","C","c","c","t","c","g","C","c", 
"c","T","t","g","a","c","a","T","t","g","g","c","g","a","c","c","c","c", 
"t","g","c","c","t","c","a","a","c","c","c","a","t","c","c","c","C","c", 
"g","t","t","a","a","g") 

を：

t_ref=translate(ref) 
t_alt=translate(alt) 

その後、私は比較することができます彼らと変更which've言う：

which((ref==alt)==FALSE) 
which((t_ref==t_alt)==FALSE) 

そこで質問がaminoaciにつながるtest DFにヌクレオチドをマークすることですdの変更。前もって感謝します。

Answer 1

使用モジュロ演算は、これがあることを指摘し、私は私の最初の試みで間違っモジュロ演算の「登録」を得たヌクレオチド配列

library(seqinr) 
test$pos %/% 3 # returns a zero-based position, so add 1 to get 1 based value 
#[1] 0 2 21 22 25 26 
t_ref[ 1+(test$pos %/% 3)] 
#[1] "M" "S" "G" "A" "R" "A" # lookup value in prot-seq 
t_alt[ 1+(test$pos %/% 3)] 
#[1] "R" "W" "A" "A" "L" "A" # test for equality to this value 
test$change <- t_ref[ 1+((test$pos-1) %/% 3)] == t_alt[ 1+((test$pos-1) %/% 3)] 
test 
#===================== 
    pos ALT REF change 
1 2 G T FALSE 
2 8 G T FALSE 
3 65 C G FALSE 
4 68 C G TRUE 
5 77 T C FALSE 
6 78 G C FALSE 

のpos列からのタンパク質配列中の位置を構築します適切に "登録されています"翻訳：

> (1:21 -1) %/% 3 
[1] 0 0 0 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6