r - 将 probeID 转换为基因符号

Question

伙计们。我是来寻求你的帮助的。

我在将 probeID 转换为 Gene.Symbol 时遇到问题

我的数据看起来像这样

               C1           C2           C3          C4          C5
200000_s_at 9.372446    9.299193    10.017991   9.181135    9.734582
200001_at   11.777132   11.692039   12.013986   11.936100   11.832065
200002_at   12.199002   12.544633   12.365026   12.026991   12.439448
200003_s_at 12.962001   12.445636   12.441083   12.809544   12.622457
200004_at   11.233249   10.961737   11.588765   11.206607   11.674372
200005_at   10.133455   10.438360   10.897712   10.653804   11.359433
200006_at   11.004593   10.584082   11.182127   11.375084   11.182136
200007_at   11.070449   10.949878   11.643648   11.581889   11.730024
200008_s_at 10.289446   10.304524   10.381671   10.136443   11.101463
200009_at   11.408603   11.114905   11.442766   11.448240   12.008252
200010_at   12.081858   11.927526   12.161929   12.299117   12.303224
200011_s_at 10.280210   10.026668   11.108151   10.371077   10.770123

如果符合以下条件，我想将我的行名（ID）更改为（基因符号）。

任何帮助，将不胜感激。

标签： r

Answer 1

假设您的注释表如下所示：

ann_table = structure(list(ID = structure(c(9L, 8L, 16L, 6L, 4L, 12L, 3L, 
10L, 5L, 13L, 2L, 11L, 1L, 7L, 15L, 17L, 14L), .Label = c("1557256_a_at", 
"1557557_at", "1557770_at", "200000_s_at", "200001_at", "200002_at", 
"200003_s_at", "200004_at", "200005_at", "200006_at", "200007_at", 
"200008_s_at", "200009_at", "200010_at", "200011_s_at", "208010_s_at", 
"235668_at"), class = "factor"), `Gene Symbol` = structure(c(3L, 
4L, 12L, 15L, 11L, 6L, 7L, 9L, 2L, 6L, 8L, 16L, 5L, 14L, 1L, 
10L, 13L), .Label = c("ARF3", "CAPNS1", "EIF3D", "EIF4G2", "GABRB1", 
"GDI2", "IPO11", "MATN1-AS1", "PARK7", "PRDM1", "PRPF8", "PTPN22", 
"RPL11", "RPL28", "RPL35", "SRP14"), class = "factor")), class = "data.frame", row.names = c("200005_at", 
"200004_at", "208010_s_at", "200002_at", "200000_s_at", "200008_s_at", 
"1557770_at", "200006_at", "200001_at", "200009_at", "1557557_at", 
"200007_at", "1557256_a_at", "200003_s_at", "200011_s_at", "235668_at", 
"200010_at"))

你展示的矩阵是：

mydata = structure(list(C1 = c(9.372446, 11.777132, 12.199002, 12.962001, 
11.233249, 10.133455, 11.004593, 11.070449, 10.289446, 11.408603, 
12.081858, 10.28021), C2 = c(9.299193, 11.692039, 12.544633, 
12.445636, 10.961737, 10.43836, 10.584082, 10.949878, 10.304524, 
11.114905, 11.927526, 10.026668), C3 = c(10.017991, 12.013986, 
12.365026, 12.441083, 11.588765, 10.897712, 11.182127, 11.643648, 
10.381671, 11.442766, 12.161929, 11.108151), C4 = c(9.181135, 
11.9361, 12.026991, 12.809544, 11.206607, 10.653804, 11.375084, 
11.581889, 10.136443, 11.44824, 12.299117, 10.371077), C5 = c(9.734582, 
11.832065, 12.439448, 12.622457, 11.674372, 11.359433, 11.182136, 
11.730024, 11.101463, 12.008252, 12.303224, 10.770123)), class = "data.frame", row.names = c("200000_s_at", 
"200001_at", "200002_at", "200003_s_at", "200004_at", "200005_at", 
"200006_at", "200007_at", "200008_s_at", "200009_at", "200010_at", 
"200011_s_at"))

对应行名的基因符号是：

as.character(ann_table[match(rownames(mydata),ann_table$ID),"Gene Symbol"])
 [1] "PRPF8"  "CAPNS1" "RPL35"  "RPL28"  "EIF4G2" "EIF3D" 
 [7] "PARK7"  "SRP14"  "GDI2"   "GDI2"   "RPL11"  "ARF3" 

或者你可以使用一个库：

library(hgu133plus2.db)
mapIds(hgu133plus2.db,keys=rownames(mydata),column=c("SYMBOL"),keytype = "PROBEID")

但在替换矩阵的行名之前，您应该检查 NA 和重复的符号。