Hi, Jim,
Thank you very much for pointing out the format issue. Here is the original
text:
===I have a text file (test.txt) with different number of columns:
0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6 1100001G20Rik%%%
Nmi 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 1700003E16Rik%%% Ascl2 Ifnar2
1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c Foxc1 Sox10
Smarca2 1810019D21Rik%%% Asb8 1810037I17Rik%%% Zfp612 1810055G02Rik%%% Nkx2-3
Maged1 Runx1 Ugp2 Elk4 Spdef Tcf19 Isl2 Gtf2i Ctnnbl1 Tcea3 Ank2 Zfp612 Creb3l1
Nupr1 3632451O06Rik Creb3l4 Lass6
I wold like to read it into R using
> test=read.csv("test.txt",sep="\t",header=FALSE)
However, when I check the r object "test", I found that all the rows have 5
columns:
> test V1 V2 V3 V4 V51
> 0610007P14Rik%%% Tcf19 Gtf2i 2 0610010O12Rik%%%
> Ivns1abp Etv6 3 1100001G20Rik%%% Nmi
> 4 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 5
> 1700003E16Rik%%% Ascl2 Ifnar2 6 1700028J19Rik%%%
> Musk Nfe2l3 7 1810011O10Rik%%% Ppp1r13b Bpnt1
> Cdkn2c Foxc18 Sox10 Smarca2 9
> 1810019D21Rik%%% Asb8 10 1810037I17Rik%%%
> Zfp612 11 1810055G02Rik%%% Nkx2-3 Maged1
> Runx1 Ugp212 Elk4 Spdef Tcf19 Isl2 Gtf2i13
> Ctnnbl1 Tcea3 Ank2 Zfp612 Creb3l114 Nupr1
> 3632451O06Rik Creb3l4 Lass6
Basically it breaks some rows into more than one rows. For example, row 7 in
the original record becomes two rows. Looks like the "test" always has 5
columns.
How does this happen? How should I fix it to make one record into one two in R
object?
==
Please let me know if it is readable now. Thank you very much for your time!
Kind regards,
Ace
On Sunday, August 27, 2017 7:25 PM, Jim Lemon <drjimle...@gmail.com> wrote:
Hi Ace,
As your example seems to have spaces as separators,
testdf<-read.table("test.txt",header=FALSE,fill=TRUE,
col.names=paste("V",1:14,sep=""),stringsAsFactors=FALSE)
By specifying the number of columns with "col.names" and using
"fill=TRUE" you can get a data frame with zero length strings where
values are missing in the input file.
Jim
On Mon, Aug 28, 2017 at 6:25 AM, Fix Ace via R-help
<r-help@r-project.org> wrote:
> Dear R community,
> I have a text file (test.txt) with different number of columns:
> 0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6 1100001G20Rik%%%
> Nmi 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 1700003E16Rik%%% Ascl2 Ifnar2
> 1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c Foxc1
> Sox10 Smarca2 1810019D21Rik%%% Asb8 1810037I17Rik%%% Zfp612 1810055G02Rik%%%
> Nkx2-3 Maged1 Runx1 Ugp2 Elk4 Spdef Tcf19 Isl2 Gtf2i Ctnnbl1 Tcea3 Ank2
> Zfp612 Creb3l1 Nupr1 3632451O06Rik Creb3l4 Lass6
> I wold like to read it into R using
> > test=read.csv("test.txt",sep="\t",header=FALSE)
> However, when I check the r object "test", I found that all the rows have 5
> columns:
>> test V1 V2 V3 V4 V51
>> 0610007P14Rik%%% Tcf19 Gtf2i 2 0610010O12Rik%%%
>> Ivns1abp Etv6 3 1100001G20Rik%%% Nmi
>> 4 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 5
>> 1700003E16Rik%%% Ascl2 Ifnar2 6 1700028J19Rik%%%
>> Musk Nfe2l3 7 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c
>> Foxc18 Sox10 Smarca2 9
>> 1810019D21Rik%%% Asb8 10 1810037I17Rik%%%
>> Zfp612 11 1810055G02Rik%%% Nkx2-3 Maged1
>> Runx1 Ugp212 Elk4 Spdef Tcf19 Isl2 Gtf2i13
>> Ctnnbl1 Tcea3 Ank2 Zfp612 Creb3l114 Nupr1 3632451O06Rik
>> Creb3l4 Lass6
> Basically it breaks some rows into more than one rows. For example, row 7 in
> the original record becomes two rows. Looks like the "test" always has 5
> columns.
> How does this happen? How should I fix it to make one record into one two in
> R object?
> Thank you very much!
> Ace
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.
