I have a .csv file as follows:
,TEST1,TEST2
ENSG00000197421,2,0
ENSG00000213753,0,2
ENSG00000168746,0,2
ENSG00000261824,3,0
ENSG00000128310,1,2
ENSG00000235091,9,4
In R, I import the file like this:
> d <- read.csv("my_file.csv", header=TRUE, row.names=1)
> d
TEST1 TEST2
ENSG00000197421 2 0
ENSG00000213753 0 2
ENSG00000168746 0 2
ENSG00000261824 3 0
ENSG00000128310 1 2
ENSG00000235091 9 4
Checking that I do not have any duplicates:
> rownames(d)
[1] "ENSG00000197421" "ENSG00000213753" "ENSG00000168746" "ENSG00000261824"
[5] "ENSG00000128310" "ENSG00000235091"
> colnames(d)
[1] "TEST1" "TEST2"
> any(duplicated(rownames(d)))
[1] FALSE
> any(duplicated(colnames(d)))
[1] FALSE
Load libraries:
> suppressMessages(library("AnnotationDbi"))
> suppressMessages(library("org.Hs.eg.db"))
Then try to convert my Ensembl row names to Symbol in place:
> rownames(d) <- mapIds(org.Hs.eg.db,keys=rownames(d),column="SYMBOL",keytype="ENSEMBL",multiVals="first")
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
missing values in 'row.names' are not allowed
NOTE: Removing the first ',' on 'my_file.csv' did not help neither.
I managed to create a new field with the converted IDs but cannot replace it to the row names:
> d$SYMBOL <- mapIds(org.Hs.eg.db,keys=rownames(d),column="SYMBOL",keytype="ENSEMBL",multiVals="first")
> d
TEST1 TEST2 SYMBOL
ENSG00000197421 2 0 GGT3P
ENSG00000213753 0 2 CENPBD1P1
ENSG00000168746 0 2 LINC01620
ENSG00000261824 3 0 LINC00662
ENSG00000128310 1 2 GALR3
ENSG00000235091 9 4 <NA>
> d_subset <- subset(d, !is.na(d$SYMBOL))
> d_subset
TEST1 TEST2 SYMBOL
ENSG00000197421 2 0 GGT3P
ENSG00000213753 0 2 CENPBD1P1
ENSG00000168746 0 2 LINC01620
ENSG00000261824 3 0 LINC00662
ENSG00000128310 1 2 GALR3
> rownames(d) <- d$SYMBOL
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
missing values in 'row.names' are not allowed
I don't get it.
4 answers
In your last line, you're still trying to assign rownames(d) <- d$SYMBOL, and not your new d_subset.
rownames(d_subset) <- d_subset$SYMBOL should work.
Alternatively, if you wish to keep all the entries, you could retain the Ensembl names when it is not mapped:
> rownames(d) <- ifelseis.na(d$SYMBOL), rownames(d), d$SYMBOL)
> d
TEST1 TEST2 SYMBOL
GGT3P 2 0 GGT3P
CENPBD1P1 0 2 CENPBD1P1
LINC01620 0 2 LINC01620
LINC00662 3 0 LINC00662
GALR3 1 2 GALR3
ENSG00000235091 9 4 <NA>
ENSG00000235091 9 4 <NA>
Here, <NA> means that you have a missing value.
It's because not all your keys (rownames(d)) in org.Hs.eg.db.
> rownames(d)
"ENSG00000197421" "ENSG00000213753" "ENSG00000168746" "ENSG00000261824" "ENSG00000128310" "ENSG00000235091"
> intersect(rownames(d),keys(org.Hs.eg.db,"ENSEMBL"))
"ENSG00000197421" "ENSG00000213753" "ENSG00000168746" "ENSG00000261824" "ENSG00000128310"
if you run this code :
mapIds(org.Hs.eg.db,keys=rownames(d)[1:5],column="SYMBOL",keytype="ENSEMBL",multiVals="first")
it's ok without any error.
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Here, missing values means
NAs, which can not be used as row names. You need to convert them to unique names (because duplicate row names are not allowed).