Hello all!
I am currently trying to sort a data frame in a particular way, but I am having
some difficulties with this. Specifically I want to sort the below dataset in
such a way that there is only one line per ProteinID and if there are multiple
GeneID or GeneName entries for a single proteinID, that they be concatenated
with a comma separating them. The way I have done it earlier worked fine for
small datasets, but as I am working with around 30,000 entries, it proved too
slow and I'm not sure how to do it in another way.
Here is an example of the input.
ProteinID
GeneID
GeneName
M-012847-00
NM_057175
NARG1
M-012847-00
NM_057175
TBDN100
M-015544-00
NM_153008
FLJ30277
M-015544-00
NM_153027
FLJ31659
M-024202-00
NM_207330
NIPAL1
M-024202-00
NM_207330
NPAL1
Here is an example showing what I want:
ProteinID
GeneID
GeneName
M-012847-00
NM_057175
NARG1, TBDN100
M-015544-00
NM_153008, NM_153027
FLJ30277, FLJ31659
M-024202-00
NM_207330
NIPAL1, NPAL1
Here is the code I have been using so far. I have only managed to get this to
work by using a loop, which I know is not the best way, but at the moment I'm
stuck.
colA <- c("M-012847-00" ,"M-012847-00" ,"M-015544-00", "M-015544-00",
"M-024202-00","M-024202-00")
colB <- c("NM_057175", "NM_057175", "NM_153008", "NM_153027", "NM_207330",
"NM_207330")
colC <- c( 'NARG1', 'TBDN100', 'FLJ30277', 'FLJ31659', 'NIPAL1', 'NPAL1')
dupes <- data.frame(ProteinID=colA, GeneID=colB, GeneName=colC)
idVec <- character()
geneIDVec <- character()
geneNameVec <- character()
dataType <- "ProteinID"
annotation <- data.frame()
for (id in unique(dupes[[dataType]])) {
print (id)
idVec <- c(idVec, id)
geneIDVec <- c(geneIDVec, paste(unique(dupes$GeneID[dupes[[dataType]] ==
id]), collapse=", "))
geneNameVec <- c(geneNameVec,
paste(unique(dupes$GeneName[dupes[[dataType]] == id]), collapse=", "))
annotation[[dataType]][annotation[[dataType]] == id] <- NA
}
filtered <- data.frame(ProteinID=idVec, GeneID=geneIDVec, GeneName=geneNameVec)
Thanks!
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