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如何操作一个列的两个部分?

genetics bioinformatics regex r

2

neuron · 技术社区 · 7 年前

我正在处理一些基因数据,我的专栏中有一篇不是我想要的格式。我不知道生物学在这里讨论了多少,但我正在尝试修正我的氨基酸在我的数据中是如何显示的。

氨基酸显然有一个名称,但它们也有一个3个字母的缩写和一个1个字母的缩写。我的数据有3个字母形式的氨基酸,但我想把它们改成1个字母的缩写。以下是我的数据示例。

 chr location           effect   impact AA_change
   1    12543 missense_variant MODERATE  p.Ala12Val
   1    52367 missense_variant MODERATE  p.Leu54Pro
   1   752347 missense_variant MODERATE  p.Met99Ser
   1   984645 missense_variant MODERATE  p.Lys34Ile
   1   989845 missense_variant MODERATE  p.Arg4Cys
   1   999854 missense_variant MODERATE  p.His43Gly
   1   999855 missense_variant MODERATE  p.Glu14Phe

dat <- structure(list(chr = c(1L, 1L, 1L, 1L, 1L, 1L, 1L), location = c(12543L, 
52367L, 752347L, 984645L, 989845L, 999854L, 999855L), effect = c("missense_variant", 
"missense_variant", "missense_variant", "missense_variant", "missense_variant", 
"missense_variant", "missense_variant"), impact = c("MODERATE", 
"MODERATE", "MODERATE", "MODERATE", "MODERATE", "MODERATE", "MODERATE"
), AA_change = c("Ala12Val", "Leu54Pro", "Met99Ser", "Lys34Ile", 
"Arg4Cys", "His43Gly", "Glu14Phe")), .Names = c("chr", "location", 
"effect", "impact", "AA_change"), row.names = c(NA, -7L), class = "data.frame")

这是一个三个字母的氨基酸列表,以及它们最好的缩写是什么。

  Ala == A
  Arg == R
  Asn == N
  Asp == D
  Cys == C
  Glu == E
  Gln == Q
  Gly == G
  His == H
  Ile == I
  Leu == L
  Lys == K
  Met == M
  Phe == F
  Pro == P
  Ser == S
  Thr == T
  Trp == W
  Tyr == Y
  Val == V

我觉得有一个简单的函数可以做这个,但我正在努力做的事情,如何做到这一点。我习惯于只改变专栏的一部分,而不是同时改变两件事。所以我要问的是我如何改变这个

Ala12Val
Leu54Pro
Met99Ser
Lys34Ile
Arg4Cys
His43Gly
Glu14Phe

为了这个

A12V
L54P
M99S
K32I
R4C
E14F

这是可以做到的吗?

3 回复 | 直到 7 年前

1

2

zx8754 7 年前

查找氨基酸,然后得到子串前3个字母和映射,提取数字,子串后3个字母和映射。然后把它们粘在一起。

# lookup map
AAmap <- setNames(c("A","R","N","D","C","E","Q","G","H","I","L","K","M","F","P","S","T","W","Y","V"),
                  c("Ala","Arg","Asn","Asp","Cys","Glu","Gln","Gly","His","Ile","Leu","Lys","Met","Phe","Pro","Ser","Thr","Trp","Tyr","Val"))

# get first 3 map to AA, get digits, get last 3 map to AA
dat$AA_change_short <-
  paste0(AAmap[ substr(dat$AA_change, 1, 3) ],
         gsub("[^\\d]+", "", dat$AA_change, perl = TRUE),
         AAmap[ substr(dat$AA_change, nchar(dat$AA_change) - 2, nchar(dat$AA_change)) ])

dat
#   chr location           effect   impact AA_change AA_change_short
# 1   1    12543 missense_variant MODERATE  Ala12Val            A12V
# 2   1    52367 missense_variant MODERATE  Leu54Pro            L54P
# 3   1   752347 missense_variant MODERATE  Met99Ser            M99S
# 4   1   984645 missense_variant MODERATE  Lys34Ile            K34I
# 5   1   989845 missense_variant MODERATE   Arg4Cys             R4C
# 6   1   999854 missense_variant MODERATE  His43Gly            H43G
# 7   1   999855 missense_variant MODERATE  Glu14Phe            E14F

2

Onyambu 7 年前

b=which(adist(dat2$V1,dat$AA_change,partial = T)==0,T)

dat$AA_change1=`regmatches<-`(dat$AA_change,gregexpr("\\D+",dat$AA_change),
                                 value=split(dat2$V3[b[,1]],b[,2]))

dat
  chr location           effect   impact AA_change AA_change1
1   1    12543 missense_variant MODERATE  Ala12Val       A12V
2   1    52367 missense_variant MODERATE  Leu54Pro       L54P
3   1   752347 missense_variant MODERATE  Met99Ser       M99S
4   1   984645 missense_variant MODERATE  Lys34Ile       I34K
5   1   989845 missense_variant MODERATE   Arg4Cys        R4C
6   1   999854 missense_variant MODERATE  His43Gly       G43H
7   1   999855 missense_variant MODERATE  Glu14Phe       E14F



dat2 = read.table(text="Ala == A
  Arg == R
  Asn == N
  Asp == D
  Cys == C
  Glu == E
  Gln == Q
  Gly == G
  His == H
  Ile == I
  Leu == L
  Lys == K
  Met == M
  Phe == F
  Pro == P
  Ser == S
  Thr == T
  Trp == W
  Tyr == Y
  Val == V")[-2]

3

2

Frank 7 年前

如果它的形式总是酸,数字,酸你可以把它分成三列,用 match 或者加入。对于data.table,这看起来像…

library(data.table)
setDT(dat)

# put your mapping into a nicer format
abbrDT = fread(header = FALSE,"
  Ala == A
  Arg == R
  Asn == N
  Asp == D
  Cys == C
  Glu == E
  Gln == Q
  Gly == G
  His == H
  Ile == I
  Leu == L
  Lys == K
  Met == M
  Phe == F
  Pro == P
  Ser == S
  Thr == T
  Trp == W
  Tyr == Y
  Val == V")[, .(abbr3 = V1, abbr1 = V3)] 

# split the column
patt = "(?<=\\d)(?=\\D)|(?<=\\D)(?=\\d)"
dat[, c("AA1", "num", "AA2") := tstrsplit(AA_change, patt, perl=TRUE)]

# substitute for each part
dat[abbrDT, on=.(AA1 = abbr3), AA1 := abbr1]
dat[abbrDT, on=.(AA2 = abbr3), AA2 := abbr1]

哪个给了

   chr location           effect   impact AA_change AA1 num AA2
1:   1    12543 missense_variant MODERATE  Ala12Val   A  12   V
2:   1    52367 missense_variant MODERATE  Leu54Pro   L  54   P
3:   1   752347 missense_variant MODERATE  Met99Ser   M  99   S
4:   1   984645 missense_variant MODERATE  Lys34Ile   K  34   I
5:   1   989845 missense_variant MODERATE   Arg4Cys   R   4   C
6:   1   999854 missense_variant MODERATE  His43Gly   H  43   G
7:   1   999855 missense_variant MODERATE  Glu14Phe   E  14   F

或者,再次组合列并删除不需要的列:

dat[, AA_change := paste0(AA1, num, AA2)]

dat[, c("AA1", "num", "AA2") := NULL]