Spaltenwerte basierend auf einer anderen Spalte

Question

ich einige Daten mit dieser Struktur haben:

## Column examples generation 
bases <- c("A", "T", "C", "G") 
ID <- c(1,2,3,4,5,6) 
SNP <- rep (c("F1", "F3", "F4"), each=length(ID)) 
Al_1 <- sample(bases, length(SNP), replace=T) 
Al_2 <- sample(bases, length(SNP), replace=T) 
tipo <- rep(c("."),length(SNP)) 

## Data frame generation: 
ArrDat <- as.data.frame(cbind(ID, SNP, Al_1, Al_2, tipo)) 
ArrDat <- data.frame(lapply(ArrDat, as.character), stringsAsFactors = F) 
OrderArr <- ArrDat[order(ArrDat$ID),] 

## Column "tipo" values: 
for (i in 1:nrow(OrderArr)) { 
if (OrderArr$Al_1[i] == "A" & OrderArr$Al_2[i] == "T"){ 
    OrderArr$tipo[i] = "a" 
    } else if (OrderArr$Al_1[i] == "A" & OrderArr$Al_2[i] == "C"){ 
    OrderArr$tipo[i] = "b" 
    } else if (OrderArr$Al_1[i] == "A" & OrderArr$Al_2[i] == "G"){ 
    OrderArr$tipo[i] = "c" 
    } else if (OrderArr$Al_1[i] == "T" & OrderArr$Al_2[i] == "A"){ 
    OrderArr$tipo[i] = "d" 
    } else if (OrderArr$Al_1[i] == "T" & OrderArr$Al_2[i] == "C"){ 
    OrderArr$tipo[i] = "e" 
    } else if (OrderArr$Al_1[i] == "T" & OrderArr$Al_2[i] == "G"){ 
    OrderArr$tipo[i] = "f" 
    } else if (OrderArr$Al_1[i] == "C" & OrderArr$Al_2[i] == "A"){ 
    OrderArr$tipo[i] = "g" 
    } else if (OrderArr$Al_1[i] == "C" & OrderArr$Al_2[i] == "T"){ 
    OrderArr$tipo[i] = "h" 
    } else if (OrderArr$Al_1[i] == "C" & OrderArr$Al_2[i] == "G"){ 
    OrderArr$tipo[i] = "i" 
    } else if (OrderArr$Al_1[i] == "G" & OrderArr$Al_2[i] == "A"){ 
    OrderArr$tipo[i] = "j" 
    } else if (OrderArr$Al_1[i] == "G" & OrderArr$Al_2[i] == "T"){ 
    OrderArr$tipo[i] = "k" 
    } else if (OrderArr$Al_1[i] == "G" & OrderArr$Al_2[i] == "C"){ 
    OrderArr$tipo[i] = "l" 
    } else if (OrderArr$Al_1[i] == "A" & OrderArr$Al_2[i] == "A"){ 
    OrderArr$tipo[i] = "STHG.A" 
    } else if (OrderArr$Al_1[i] == "T" & OrderArr$Al_2[i] == "T"){ 
    OrderArr$tipo[i] = "STHG.T" 
    } else if (OrderArr$Al_1[i] == "C" & OrderArr$Al_2[i] == "C"){ 
    OrderArr$tipo[i] = "STHG.C" 
    } else if (OrderArr$Al_1[i] == "G" & OrderArr$Al_2[i] == "G"){ 
    OrderArr$tipo[i] = "STHG.G" 
    } else {OrderArr$tipo[i] = "x"} 
} 

Hier ist ein Beispiel für die Daten:

ID SNP Al_1 Al_2 tipo 
1 1 F1 T A  d 
7 1 F3 C A  g 
13 1 F4 G C  l 
2 2 F1 T T STHG.T 
8 2 F3 C C STHG.C 
14 2 F4 C C STHG.C 

Mein Problem sind die OrderArr $ tipo Werte für diese Al_1 -Al_2 Kombinationen: AA, TT, CC oder GG. Diese Kombinationen können einen OrderArr $ tipo Wert gleich anderen Zeilen haben mit dem gleichen OrderArr $ SNP-Wert, so dass die Daten, die ich vor setzen sollte:

ID SNP Al_1 Al_2 tipo 
1 1 F1 T A  d 
7 1 F3 C A  g 
13 1 F4 G C  l 
2 2 F1 T T  d 
8 2 F3 C C  g 
14 2 F4 C C  l 

Wie kann ich diese auf den Code implementieren?

Vielen Dank.

Answer 1

Ich habe einen Datenrahmen erstellt, wo jeder SNP nur eine Kombination von Al_1 und Al_2 hat.

ID SNP Al_1 Al_2 combo tipo 
1 1 F1 A T AT a 
2 1 F4 G G GG z 
3 1 D2 C T CT h 
4 1 D4 T C TC e 
5 1 HY7 A A AA z 
6 1 HY66 T G TG f 
7 1 XZD1 C A CA g 
8 1 XZD33 G A GA j 
9 2 F1 A A AA z 
10 2 F4 C G CG i 
11 2 D2 C C CC z 
12 2 D4 T C TC e 
13 2 HY7 A A AA z 
14 2 HY66 G G GG z 
15 2 XZD1 C A CA g 
16 2 XZD33 G A GA j 
17 3 F1 T T TT z 
18 3 F4 C C CC z 
19 3 D2 C T CT h 
20 3 D4 T C TC e 
21 3 HY7 A C AC b 
22 3 HY66 G G GG z 
23 3 XZD1 A A AA z 
24 3 XZD33 A A AA z 
25 4 F1 A T AT a 
26 4 F4 C G CG i 
27 4 D2 C T CT h 
28 4 D4 T T TT z 
29 4 HY7 C C CC z 
30 4 HY66 T T TT z 
31 4 XZD1 C A CA g 
32 4 XZD33 A A AA z 
33 5 F1 T T TT z 
34 5 F4 C G CG i 
35 5 D2 T T TT z 
36 5 D4 T T TT z 
37 5 HY7 A A AA z 
38 5 HY66 T G TG f 
39 5 XZD1 A A AA z 
40 5 XZD33 G G GG z 
41 6 F1 A T AT a 
42 6 F4 G G GG z 
43 6 D2 T T TT z 
44 6 D4 C C CC z 
45 6 HY7 C C CC z 
46 6 HY66 T T TT z 
47 6 XZD1 C C CC z 
48 6 XZD33 G A GA j 

Und ich denke, ich habe eine Antwort auf Ihre Frage.

data$combo <- paste0(data$Al_1, data$Al_2) 
snp <- unique(data$SNP) 

for (i in 1:nrow(data)){ 
    if(data$Al_1[i] == data$Al_2[i]) data$tipo[i] ='z' 
    else if (data$Al_1[i] == 'A') { 
    if (data$Al_2[i] == 'T') data$tipo[i] = 'a' 
    else if (data$Al_2[i] == 'C') data$tipo[i] = 'b' 
    else if (data$Al_2[i] == 'G') data$tipo[i] = 'c' 
    } 
    else if (data$Al_1[i] == 'T') { 
    if (data$Al_2[i] == 'A') data$tipo[i] = 'd' 
    else if (data$Al_2[i] == 'C') data$tipo[i] = 'e' 
    else if (data$Al_2[i] == 'G') data$tipo[i] = 'f' 
    } 
    else if (data$Al_1[i] == 'C') { 
    if (data$Al_2[i] == 'A') data$tipo[i] = 'g' 
    else if (data$Al_2[i] == 'T') data$tipo[i] = 'h' 
    else if (data$Al_2[i] == 'G') data$tipo[i] = 'i' 
    } 
    else if (data$Al_1[i] == 'G') { 
    if (data$Al_2[i] == 'A') data$tipo[i] = 'j' 
    else if (data$Al_2[i] == 'T') data$tipo[i] = 'k' 
    else if (data$Al_2[i] == 'C') data$tipo[i] = 'l' 
    } 
} 

ord.data <- data 
ord.data2 <- data.frame() 

for (j in 1:length(snp)){ 
    temp <- ord.data[as.numeric(as.factor(ord.data$SNP)) == j, ] 
    for (h in 1:nrow(temp)){ 
    if (temp$tipo[h] == 'z') { 
     if (temp$Al_1[h] == 'A') { 
     tempi <- subset(temp, tipo != 'z') 
     letra <- unique(tempi$tipo) 
     temp$tipo[h] = letra 
     } 
     else if (temp$Al_1[h] == 'T') { 
     tempi <- subset(temp, tipo != 'z') 
     letra <- unique(tempi$tipo) 
     temp$tipo[h] = letra 
     } 
     else if (temp$Al_1[h] == 'C') { 
     tempi <- subset(temp, tipo != 'z') 
     letra <- unique(tempi$tipo) 
     temp$tipo[h] = letra 
     } 
     else if (temp$Al_1[h] == 'G') { 
     tempi <- subset(temp, tipo != 'z') 
     letra <- unique(tempi$tipo) 
     temp$tipo[h] = letra 
     } 
    } 
    } 
    ord.data2 <- rbind(ord.data2, temp) 
}