How to select columns containing specific text in R

Question

Hi to all,

I have data like this in table

IND	snp1	snp2	snp3	snp4	snp5
1	A/G	T/T	T/C	G/C	G/G
2	A/A	C/C	G/G	G/G	A/A
3	T/T	G/G	C/C	C/C	T/T

and I wish to select only snp1,snp3, and snp4 containing different letters combinations like A/G, T/C AND G/C. can anyone help me to select only those columns? any help in this regard is highly appreciated

Thanks in advance

Answer 1

Hi,

You can use the select method to extract particular columns and rows. According to your dataset, you can use the below-given code.

> df
  IND snp1 snp2 snp3 snp4 snp5
1   1  A/G  T/T  T/C  G/C  G/G
2   2  A/A  C/C  G/G  G/G  A/A
3   3  T/T  G/G  C/C  C/C  T/T

> select(df, snp1,snp3,snp4)[1,1:3]
  snp1 snp3 snp4
1  A/G  T/C  G/C

I hope this will give you the approach.

Comments

Hi

Thanks for sharing your time to help me. Yes i can do that using select function but my case is different i have 20,000 columns and i do not which column contains this type of character (A/T,A/G,A/C,T/A,T/G,T/C,G/A,G/T,G/C,C/A,C/T,C/G), first i need identify columns containing these characters A/T,A/G,A/C,T/A,T/G,T/C,G/A,G/T,G/C,C/A,C/T,C/G in my data file and extracting them into different file. I hope i explained well. once again thanks lot for your help.

---

i tried this code to extract rows containing specific text across columns

collist <- c("SNP1","SNP2","SNP3","SNP4","SNP5")
sel <- apply(red[,collist],1,function(row) length(grep("T/C",row))>0)
red[sel,]

now i want extract columns containing "T/C" across columns SNP1 to SNP5 and i applied function like this

sel <- apply(red[,collist],2,function(cols) length(grep("A/G",cols))>0)
red[sel,]

but this is not working for me to get required out put i.e. snp3. can anyone help to sort this out?

thanks in advance for your help

---

Hi,

Can you explain your query a little bit more?

---

Dear MD

good morning

what ever you did is right and i can give column numbers if my data is small but now i have more than 20000 columns and i do not know which columns of my data having these  this type of character (A/T,A/G,A/C,T/A,T/G,T/C,G/A,G/T,G/C,C/A,C/T,C/G. i would like to mention columns containing these characters instead of column numbers and able to subset those columns only having above characters..

I hope i explained well

Thanks in advance

---

Hi,

You need to create your own customized script. Like your script will check every column and search your pattern if it matches then append the column name in a list otherwise it will skip that column.