Thanks a lot. It works great now!
________________________________
Cc: R help <r-help@r-project.org>
Sent: Friday, September 13, 2013 11:46 PM
Subject: Re: [R] problem with grep under loop
Hi,
dat1<- read.table("gao.txt",sep="",header=FALSE,stringsAsFactors=FALSE)
dat1
# V1 V2 V3 V4 V5 V6 V7 V8
#1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
#2 - - u C.3 C.3.1 100 1.000000 0.000000
#3 - - u C.2 C.2.1 100 1.000000 0.000000
#4 - - u C.4 C.4.1 100 1.000000 0.000000
#5 - - u C.1 C.1.1 100 1.000000 0.000000
#6 - - u C.5 C.5.1 100 1.000000 0.000000
# V9 V10 V11 V12 V13
#1 FPKM_conf_hi cov len major_iso_id ref_match_len
#2 0.000000 0.056682 96 C.3.1 -
#3 0.000000 0.058453 99 C.2.1 -
#4 0.000000 0.059634 101 C.4.1 -
#5 0.000000 0.059634 101 C.2.1 -
#6 0.000000 0.059634 101 C.5.1 -
You should read the dataset with read.table(...., header=TRUE) as your dataset
already had colnames.
for(i in 1:nrow(dat1)){if(length(grep(dat1[i,4],dat1[i,12])==1)!=0) print("Y")}
[1] "Y"
[1] "Y"
[1] "Y"
[1] "Y"
A.K.
Sorry about that. I will try to reformat my question.
I have a dataset with format like:
----------------------------------
> head(data)
V1 V2 V3 V4 V5 V6 V7 V8
1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
2 - - u C.3 C.3.1 100 1.000000 0.000000
3 - - u C.2 C.2.1 100 1.000000 0.000000
4 - - u C.4 C.4.1 100 1.000000 0.000000
5 - - u C.1 C.1.1 100 1.000000 0.000000
6 - - u C.5 C.5.1 100 1.000000 0.000000
V9 V10 V11 V12 V13
1 FPKM_conf_hi cov len major_iso_id ref_match_len
2 0.000000 0.056682 96 C.3.1 -
3 0.000000 0.058453 99 C.2.1 -
4 0.000000 0.059634 101 C.4.1 -
5 0.000000 0.059634 101 C.7.1 -
6 0.000000 0.059634 101 C.5.1 -
---------------------
here column5 has extra ".1" compared with column4, and column12
might be different from column5 with similar format, for example row 5;
but most of them (column5 and column12) are the same (like the rest of
the rows) . I am trying to find the different ones by using "grep"
this data has a dimension of 52086 by 13
so my ran the following code:
------------
> dim(data)
[1] 52086 13
> if(grep(data[3,4],data[3,12])==1) print("Y")
[1] "Y"
> for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print ("Y")}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print("Y") :
argument is of length zero
-----------
here I tested the grep command first and it looks ok. However, when I put it in
for loop, error message came:
argument is of length zero
Could you please help me figure out what happened here?
Thanks a lot for your help.
----- Original Message -----
To: "r-help@r-project.org" <r-help@r-project.org>
Cc:
Sent: Friday, September 13, 2013 9:29 PM
Subject: [R] problem with grep under loop
I am just testing the possibility of using grep under for loop:
>for(i in 1:10){grep("a",letters)}
nothing came out;
when I ran:
>grep("a",letters),
I got "1"
so in my for loop, I expected to see ten "1"s, but I did not.
Could anybody help me to figure out why? Thanks a lot for your help.
Capricy
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
