problem with order function

Question

[yasjas]

Hello guys,

I have some problems with the order function in R.What I am trying to do is to order by ("chr-name","chr-start","chr-end)

When I tried with the three it gave me just the two first columns, when I tried with only "chr-start", it worked but not as I wanted

Here is what I did and hopefully someone has an idea on how to do it

First try:

col=c("chr-nameRM","chr-startRM")
ordered1 <- chr_cancer [with(chr_cancer,order(col)),]

result:

chr-nameRM chr-startRM chr-endRM
      chr1      839792    839815
      chr1      859231    859271

second try:

ordered2 <- chr_cancer[order(chr_cancer[["chr-nameRM"]]),]

Result: This gave me half what I wanted as the chr names are not in order because what I am trying to do next is to compare other files.So if anyone has an idea I would be grateful

Thanks

[PoGibas]

Nobody would be able to answer this question without example data. And why do you use double brackets ([["chr-nameRM"]])? If you're going to compare multiple tables maybe just simple setkey is all what you need.

[Sean Davis]

While I answered your "literal" question, can you elaborate on what you mean by "compare to other files"? How are you doing the comparison?

[yasjas]

Hello, sorry for the late reply

Well I am using seqmonk as well and wanted to see if I come up with the same result files using R

Answer 1

[Sean Davis]

Untested, but something like this might work.

ordered = chr_cancer[order(chr_cancer[,"chr-nameRM"],chr_cancer[,"chr-startRM"],chr_cancer[,"chr-endRM"]),]

If you want to save yourself some headaches, don't use special characters (like -) in column names. Also, dplyr and data.table are your friends, so you might want to play with those in your free time to accomplish the same task.