Remove lines from a toptable that have an empty ID (symbol)

Question

[mannoulag1]

Hi,

How to remove lines (genes) from a toptable tt that have an empty ID (symbol)? These genes are not annotated and I would like to remove them from the toptable.

the columns are:

row.names, ID, logFC, AverExpr, …

Thanks

[WouterDeCoster]

What have you tried? This is a quite basic R question on slicing/subsetting a dataframe.

[zx8754]

Basic R questions are more relevant to StackOverflow:

• Filter data.frame rows by a logical condition

Answer 1

[ahmad mousavi]

Hi

notEmpty <- subset(tt, tt$ID !="")

[zx8754]

No need to call tt in subset again, try:

notEmpty <- subset(tt, ID != "")

Also note, from ?subset manual:

This is a convenience function intended for use interactively. For programming it is better to use the standard subsetting functions like [, and in particular the non-standard evaluation of argument subset can have unanticipated consequences.

So the preferred way would be:

notEmpty <- tt[ tt$ID != "", ]

[ahmad mousavi]

yeah that's work too, nice code !!

[mannoulag1]

thank you ahmad mousavi

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.