比較

Question

當我有這些數據（DAT2）

CHOM POS REF  ALT  ALT1 ALT2 ... 
1 121 A  AA   AT  0 
2 254 GCGC GCGCG  AGCG  0 
3 214 C  T   0   0 

我需要來標記每一行或ALT，ALT1和ALT2每一個細胞。與任何這些變異SNP的，刪除，插入。

這將解釋如何SNP和刪除和插入區分..

REF ALT1 ALT2 
A  T  NA = SNP 
AT T   = deletion 
CG CGG  = insertion 
ATT AT   = deletion 

也許輸出會是這樣

CHOM POS REF  ALT    ALT1   ALT2 ... 
    1 121 A  deletion   insertion  0 
    2 254 GCGC  insertion   SNP   0 

Answer 1

一個簡單的方法是隻用nchar看在每個字符串的長度。該假設數據已經預先消毒

例如：

ref <- c("A", "AT", "CG", "ATT") 
alt1 <- c("T", "T", "CGG", "AT") 

ref.length <- nchar(ref) 
alt1.length <- nchar(alt1) 

variations <- ifelse(ref.length==alt1.length, "SNP", 
        ifelse(ref.length>alt1.length, "deletion", 
          "insertion")) 

這給

> cbind(ref, alt1, variations) 
    ref alt1 variations 
A "A" "T" "SNP"  
AT "AT" "T" "deletion" 
CG "CG" "CGG" "insertion" 
ATT "ATT" "AT" "deletion"