R: remove rows by a list of rownames

Question

[silvi_free88]

Dear all, I am having a bit of trouble trying to remove rows in a table by its rowname. I would be very graceful if you could check if i am doing something wrong. Here is what i'm doing:

> data = read.table("path/to/my/file/file", header=T, row.names=1, com='')
> head(data)
                    apo1_LO apo2_LO apo3_LO apo4_LO lux1_LO lux2_LO lux3_LO
comp230955_c0_seq10    0.00    8.05    8.15   32.91    0.00   38.41    0.00
comp135535_c0_seq1     1.00    0.00    0.00    0.00    0.00    0.00    0.00
comp222610_c5_seq4     4.96    8.21    1.84    5.57   14.59    6.54    6.51
comp227842_c8_seq3    93.53  131.08   79.54  198.85  166.32  108.80   43.79
comp230019_c3_seq1   141.97  355.04  142.11   71.02  497.84  424.01  212.69
comp215198_c1_seq3    18.27   28.28   10.52    0.00   64.35    0.00    0.00
                    lux4_LO WT1_LO WT2_LO WT3_LO WT4_LO
comp230955_c0_seq10   17.45  16.59   0.00   0.00   0.00
comp135535_c0_seq1     0.00   0.00   1.00   1.00   0.00
comp222610_c5_seq4     3.78   5.43  11.87   6.01   1.99
comp227842_c8_seq3   125.63  45.37  34.13 103.42  67.96
comp230019_c3_seq1   142.03  70.95  70.54  70.93 142.23
comp215198_c1_seq3    21.05  17.74   0.00  19.66   0.00

> dim(data)
[1] 171471     12

> vf = read.table("vf_IDs", header=T, sep="\t")
> remove= vf$contig_id # list of rownames I would like to remove from file "data"

> head(remove)
[1] comp168081_c0_seq1  comp168081_c1_seq1  comp168081_c2_seq1
[4] comp168081_c3_seq1  comp3015455_c0_seq1 comp13879_c0_seq1  
78 Levels: comp105265_c0_seq1 comp105265_c1_seq1 ... comp80665_c0_seq1

> datawithoutVF = data[ !(rownames(data) %in% remove), ]
> dim(datawithoutVF)
[1] 171417     12

# The dimensions of the new table, "datawithoutVF" is the same as the original "data". So it seems any row has been deleted. I checked then if at least one of the rowname of the list was in the original data.

> any(row.names(data) == 'comp168081_c2_seq1')
[1] TRUE

# But checking in the "fileterd" table I don't find it.

> any(row.names(datawithoutVF) == 'comp168081_c2_seq1')
[1] FALSE

It seems that it is removing the rownames but not the actual row. I guess i am missing something important but I do not understand what is going on.

How could I remove the entire row by its rowname?

Many thanks for your help!

[Devon Ryan]

datawithoutVF does have fewer rows than data in your example (54 fewer rows, to be exact).

[silvi_free88]

True!! Oh dear, I am dyslexic and did not see it! Thanks to point it out :)

No problem then.

Answer 1

[silvi_free88]

SOLVED:

All the options work!

datawithoutVF = data[which(rownames(data) %nin% remove), ]
datawithoutVF = data[!row.names(data)%in%remove,]
datawithoutVF = data[ !(row.names(data) %in% remove), ]

Thanks to all!

[bmpbowen]

Make sure to upvote the solutions that worked for you.

Answer 2

[bmpbowen]

Haven't tested it with your data, but try using the %nin% command from the Hmisc package:

install.packages("Hmisc")
library("Hmisc")
datawithoutVF = data[which(rownames(data) %nin% remove), ]

[silvi_free88]

Hi, thanks for the replay. I tried and I found the same problem:

> datawithoutVF = data[which(rownames(data) %nin% remove), ]
> dim(datawithoutVF)
[1] 171417     12
> any(row.names(datawithoutVF) == 'comp168081_c2_seq1')
[1] FALSE

However, I tried also the negative command, like this:

> datawithoutVF = data[-which(rownames(data) %nin% remove), ]
> dim(datawithoutVF)
[1] 54 12

> any(row.names(datawithoutVF) == 'comp168081_c2_seq1')
[1] TRUE

In this case it seems that is removing the rows but keeping only the ones in the list.

[bmpbowen]

What about

datawithoutVF = data[-which(rownames(data) %in% remove), ]

Answer 3

[edwards]

I think you need to put in row.names() instead of rownames(). Also the parentheses may be throwing it off. Try this instead.

datawithoutVF = data[!row.names(data)%in%remove,]

[silvi_free88]

Thanks for the reply! Not working though:

> datawithoutVF = data[!row.names(data)%in%remove,]
> dim(datawithoutVF)
[1] 171417     12

[Devon Ryan]

rownames() and row.names() will typically return the same thing. row.names() is a more extensible method, though.