Lisann Lisann - 1 month ago 6
R Question

Merge or combine by rownames

In the example below I have two datasets (Z and A). I want to merge or combine these sets by the ILMN numbers. If there is no match, fill in NA.

z <- matrix(c(0,0,1,1,0,0,1,1,0,0,0,0,1,0,1,1,0,1,1,1,1,0,0,0,"RND1","WDR", "PLAC8","TYBSA","GRA","TAF"), nrow=6,
dimnames=list(c("ILMN_1651838","ILMN_1652371","ILMN_1652464","ILMN_1652952","ILMN_1653026","ILMN_1653103"),c("A","B","C","D","symbol")))

t<-matrix(c("GO:0002009", 8, 342, 1, 0.07, 0.679, 0, 0, 1, 0,
"GO:0030334", 6, 343, 1, 0.07, 0.065, 0, 0, 1, 0,
"GO:0015674", 7, 350, 1, 0.07, 0.065, 1, 0, 0, 0), nrow=10, dimnames= list(c("GO.ID","LEVEL","Annotated","Significant","Expected","resultFisher","ILMN_1652464","ILMN_1651838","ILMN_1711311","ILMN_1653026")))


The result will be like this:

[,1] [,2] [,3] [,4]
GO.ID "GO:0002009" "GO:0030334" "GO:0015674" NA
LEVEL "8" "6" "7" NA
Annotated "342" "343" "350" NA
Significant "1" "1" "1" NA
Expected "0.07" "0.07" "0.07" NA
resultFisher "0.679" "0.065" "0.065" NA
ILMN_1652464 "0" "0" "1" PLAC8
ILMN_1651838 "0" "0" "0" RND1
ILMN_1711311 "1" "1" "0" NA
ILMN_1653026 "0" "0" "0" GRA

Answer

Use match to return your desired vector, then cbind it to your matrix

cbind(t, z[, "symbol"][match(rownames(t), rownames(z))])

             [,1]         [,2]         [,3]         [,4]   
GO.ID        "GO:0002009" "GO:0030334" "GO:0015674" NA     
LEVEL        "8"          "6"          "7"          NA     
Annotated    "342"        "343"        "350"        NA     
Significant  "1"          "1"          "1"          NA     
Expected     "0.07"       "0.07"       "0.07"       NA     
resultFisher "0.679"      "0.065"      "0.065"      NA     
ILMN_1652464 "0"          "0"          "1"          "PLAC8"
ILMN_1651838 "0"          "0"          "0"          "RND1" 
ILMN_1711311 "1"          "1"          "0"          NA     
ILMN_1653026 "0"          "0"          "0"          "GRA"  

PS. Be warned that t is base R function that is used to transpose matrices. By creating a variable called t, it can lead to confusion in your downstream code.

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