I have read data table and out.list in R like this:
data =
read.table("Mymensingh_root_relative.percent.COUNT.txt",header=T,sep='\t',check.names=F)
otu.list =
read.table("root_differential.OTU.list.txt",header=T,sep='\t',check.names=F)
these both are tab delimited text files.
*
*
*Thanks*
*Yogesh*
On Sun, Jun 23, 2019 at 4:22 PM Yogesh Gupta <nabiyog...@gmail.com
<mailto:nabiyog...@gmail.com>> wrote:
Hi Rui,
Thanks for your help. but still I did not able to get the data.
> dput(head(data))
structure(list(`Root-1.S35.L001` = c(0, 0, 0, 0, 0, 0.0467945718296678
), `Root-10.S75.L001` = c(0, 0, 0, 0, 0, 0), `Root-13.S5.L001` = c(0,
0, 0, 0, 0, 0), `Root-14.S16.L001` = c(0, 0, 0, 0, 0, 0),
`Root-17.S26.L001` = c(0,
0, 0, 0, 0, 0), `Root-18.S36.L001` = c(0, 0, 0, 0, 0, 0),
`Root-19.S46.L001` = c(0,
0, 0, 0, 0, 0), `Root-22.S56.L001` = c(0, 0, 0, 0, 0, 0),
`Root-24.S66.L001` = c(0,
0, 0, 0, 0, 0), `Root-25.S76.L001` = c(0, 0, 0, 0, 0, 0),
`Root-26.S6.L001` = c(0,
0, 0, 0, 0, 0), `Root-27.S17.L001` = c(0.0293745480838756, 0,
0, 0, 0, 0), `Root-3.S45.L001` = c(0, 0, 0, 0, 0, 0),
`Root-30.S27.L001` = c(0,
0, 0, 0, 0, 0), `Root-32.S37.L001` = c(0, 0, 0, 0, 0, 0),
`Root-34.S47.L001` = c(0,
0, 0, 0, 0, 0), `Root-39.S57.L001` = c(0, 0, 0, 0, 0, 0),
`Root-4.S55.L001` = c(0,
0, 0, 0, 0, 0), `Root-40.S67.L001` = c(0.0189409882986783, 0,
0, 0, 0, 0), `Root-41.S77.L001` = c(0.0171320884015762, 0, 0,
0.0202470135654991, 0, 0), `Root-43.S7.L001` = c(0, 0, 0, 0,
0, 0), `Root-45.S18.L001` = c(0, 0, 0, 0, 0, 0), `Root-47.S28.L001`
= c(0,
0, 0, 0, 0, 0), `Root-50.S38.L001` = c(0, 0, 0, 0, 0, 0),
`Root-51.S48.L001` = c(0,
0, 0, 0, 0, 0), `Root-54.S58.L001` = c(0.0080481457966323, 0,
0, 0, 0, 0), `Root-9.S65.L001` = c(0.00744125132082211, 0, 0,
0, 0, 0), Root.11.S5 = c(0, 0, 0, 0, 0, 0), Root.12.S16 = c(0,
0, 0, 0, 0, 0), Root.15.S26 = c(0, 0, 0, 0, 0, 0), Root.16.S36 = c(0,
0, 0, 0, 0, 0), Root.2.S35 = c(0, 0, 0, 0, 0, 0), Root.20.S46 = c(0,
0, 0, 0, 0, 0), Root.21.S56 = c(0, 0, 0, 0, 0, 0), Root.23.S66 = c(0,
0, 0, 0.0123632317487791, 0, 0), Root.28.S76 = c(0, 0, 0, 0,
0, 0), Root.29.S6 = c(0, 0, 0, 0, 0, 0), Root.31.S17 = c(0, 0,
0, 0, 0, 0), Root.33.S27 = c(0.0165520894254218, 0, 0, 0, 0,
0), Root.35.S37 = c(0, 0, 0, 0, 0, 0), Root.36.S47 = c(0,
0.00731421884142774,
0, 0, 0, 0), Root.37.S57 = c(0.00668627975394491, 0, 0,
0.00780065971293572,
0, 0), Root.38.S67 = c(0, 0, 0, 0, 0, 0), Root.42.S77 =
c(0.00368785956630772,
0, 0, 0, 0.00553178934946157, 0), Root.44.S7 = c(0, 0,
0.0306968177632252,
0, 0, 0), Root.46.S18 = c(0, 0, 0, 0, 0, 0), Root.48.S28 = c(0,
0, 0, 0, 0, 0), Root.49.S38 = c(0, 0.0133380016339052, 0, 0,
0, 0), Root.5.S45 = c(0, 0, 0, 0, 0, 0), Root.52.S48 = c(0, 0,
0, 0, 0, 0), Root.53.S58 = c(0, 0, 0, 0, 0, 0), Root.6.S55 =
c(0.0150072892547809,
0, 0, 0, 0, 0), Root.7.S65 = c(0, 0, 0, 0, 0, 0), Root.8.S75 = c(0,
0, 0, 0.0062986835751328, 0, 0)), row.names =
c("71f84e7910006f22684121564206e8ca",
"03b167b9f86f2519b4263b4125377eed", "54e204fb99c80764e964456dadd6a0e5",
"55cd1fc570879d645bbf7a3642e9b0a8", "65f5c31e12c277aec319e2096463f9d2",
"7bed62f0fef250fd831dcf13bf43f4fc"), class = "data.frame")
> i <- row.names(data) %in% otu.list
> data[i, ]
[1] Root-1.S35.L001 Root-10.S75.L001 Root-13.S5.L001
Root-14.S16.L001
[5] Root-17.S26.L001 Root-18.S36.L001 Root-19.S46.L001
Root-22.S56.L001
[9] Root-24.S66.L001 Root-25.S76.L001 Root-26.S6.L001
Root-27.S17.L001
[13] Root-3.S45.L001 Root-30.S27.L001 Root-32.S37.L001 Root-34.S47.L001
[17] Root-39.S57.L001 Root-4.S55.L001 Root-40.S67.L001 Root-41.S77.L001
[21] Root-43.S7.L001 Root-45.S18.L001 Root-47.S28.L001 Root-50.S38.L001
[25] Root-51.S48.L001 Root-54.S58.L001 Root-9.S65.L001 Root.11.S5
[29] Root.12.S16 Root.15.S26 Root.16.S36 Root.2.S35
[33] Root.20.S46 Root.21.S56 Root.23.S66 Root.28.S76
[37] Root.29.S6 Root.31.S17 Root.33.S27 Root.35.S37
[41] Root.36.S47 Root.37.S57 Root.38.S67 Root.42.S77
[45] Root.44.S7 Root.46.S18 Root.48.S28 Root.49.S38
[49] Root.5.S45 Root.52.S48 Root.53.S58 Root.6.S55
[53] Root.7.S65 Root.8.S75
<0 rows> (or 0-length row.names)
Thanks
On Sun, Jun 23, 2019 at 4:20 PM Yogesh Gupta <nabiyog...@gmail.com
<mailto:nabiyog...@gmail.com>> wrote:
Hi Rui,
Thanks for your help. but still I did able to get the data.
> dput(head(data))
structure(list(`Root-1.S35.L001` = c(0, 0, 0, 0, 0,
0.0467945718296678
), `Root-10.S75.L001` = c(0, 0, 0, 0, 0, 0), `Root-13.S5.L001` =
c(0,
0, 0, 0, 0, 0), `Root-14.S16.L001` = c(0, 0, 0, 0, 0, 0),
`Root-17.S26.L001` = c(0,
0, 0, 0, 0, 0), `Root-18.S36.L001` = c(0, 0, 0, 0, 0, 0),
`Root-19.S46.L001` = c(0,
0, 0, 0, 0, 0), `Root-22.S56.L001` = c(0, 0, 0, 0, 0, 0),
`Root-24.S66.L001` = c(0,
0, 0, 0, 0, 0), `Root-25.S76.L001` = c(0, 0, 0, 0, 0, 0),
`Root-26.S6.L001` = c(0,
0, 0, 0, 0, 0), `Root-27.S17.L001` = c(0.0293745480838756, 0,
0, 0, 0, 0), `Root-3.S45.L001` = c(0, 0, 0, 0, 0, 0),
`Root-30.S27.L001` = c(0,
0, 0, 0, 0, 0), `Root-32.S37.L001` = c(0, 0, 0, 0, 0, 0),
`Root-34.S47.L001` = c(0,
0, 0, 0, 0, 0), `Root-39.S57.L001` = c(0, 0, 0, 0, 0, 0),
`Root-4.S55.L001` = c(0,
0, 0, 0, 0, 0), `Root-40.S67.L001` = c(0.0189409882986783, 0,
0, 0, 0, 0), `Root-41.S77.L001` = c(0.0171320884015762, 0, 0,
0.0202470135654991, 0, 0), `Root-43.S7.L001` = c(0, 0, 0, 0,
0, 0), `Root-45.S18.L001` = c(0, 0, 0, 0, 0, 0),
`Root-47.S28.L001` = c(0,
0, 0, 0, 0, 0), `Root-50.S38.L001` = c(0, 0, 0, 0, 0, 0),
`Root-51.S48.L001` = c(0,
0, 0, 0, 0, 0), `Root-54.S58.L001` = c(0.0080481457966323, 0,
0, 0, 0, 0), `Root-9.S65.L001` = c(0.00744125132082211, 0, 0,
0, 0, 0), Root.11.S5 = c(0, 0, 0, 0, 0, 0), Root.12.S16 = c(0,
0, 0, 0, 0, 0), Root.15.S26 = c(0, 0, 0, 0, 0, 0), Root.16.S36 =
c(0,
0, 0, 0, 0, 0), Root.2.S35 = c(0, 0, 0, 0, 0, 0), Root.20.S46 =
c(0,
0, 0, 0, 0, 0), Root.21.S56 = c(0, 0, 0, 0, 0, 0), Root.23.S66 =
c(0,
0, 0, 0.0123632317487791, 0, 0), Root.28.S76 = c(0, 0, 0, 0,
0, 0), Root.29.S6 = c(0, 0, 0, 0, 0, 0), Root.31.S17 = c(0, 0,
0, 0, 0, 0), Root.33.S27 = c(0.0165520894254218, 0, 0, 0, 0,
0), Root.35.S37 = c(0, 0, 0, 0, 0, 0), Root.36.S47 = c(0,
0.00731421884142774,
0, 0, 0, 0), Root.37.S57 = c(0.00668627975394491, 0, 0,
0.00780065971293572,
0, 0), Root.38.S67 = c(0, 0, 0, 0, 0, 0), Root.42.S77 =
c(0.00368785956630772,
0, 0, 0, 0.00553178934946157, 0), Root.44.S7 = c(0, 0,
0.0306968177632252,
0, 0, 0), Root.46.S18 = c(0, 0, 0, 0, 0, 0), Root.48.S28 = c(0,
0, 0, 0, 0, 0), Root.49.S38 = c(0, 0.0133380016339052, 0, 0,
0, 0), Root.5.S45 = c(0, 0, 0, 0, 0, 0), Root.52.S48 = c(0, 0,
0, 0, 0, 0), Root.53.S58 = c(0, 0, 0, 0, 0, 0), Root.6.S55 =
c(0.0150072892547809,
0, 0, 0, 0, 0), Root.7.S65 = c(0, 0, 0, 0, 0, 0), Root.8.S75 = c(0,
0, 0, 0.0062986835751328, 0, 0)), row.names =
c("71f84e7910006f22684121564206e8ca",
"03b167b9f86f2519b4263b4125377eed",
"54e204fb99c80764e964456dadd6a0e5",
"55cd1fc570879d645bbf7a3642e9b0a8",
"65f5c31e12c277aec319e2096463f9d2",
"7bed62f0fef250fd831dcf13bf43f4fc"), class = "data.frame")
> i <- row.names(data) %in% otu.list
> data[i, ]
[1] Root-1.S35.L001 Root-10.S75.L001 Root-13.S5.L001
Root-14.S16.L001
[5] Root-17.S26.L001 Root-18.S36.L001 Root-19.S46.L001
Root-22.S56.L001
[9] Root-24.S66.L001 Root-25.S76.L001 Root-26.S6.L001
Root-27.S17.L001
[13] Root-3.S45.L001 Root-30.S27.L001 Root-32.S37.L001
Root-34.S47.L001
[17] Root-39.S57.L001 Root-4.S55.L001 Root-40.S67.L001
Root-41.S77.L001
[21] Root-43.S7.L001 Root-45.S18.L001 Root-47.S28.L001
Root-50.S38.L001
[25] Root-51.S48.L001 Root-54.S58.L001 Root-9.S65.L001 Root.11.S5
[29] Root.12.S16 Root.15.S26 Root.16.S36 Root.2.S35
[33] Root.20.S46 Root.21.S56 Root.23.S66 Root.28.S76
[37] Root.29.S6 Root.31.S17 Root.33.S27 Root.35.S37
[41] Root.36.S47 Root.37.S57 Root.38.S67 Root.42.S77
[45] Root.44.S7 Root.46.S18 Root.48.S28 Root.49.S38
[49] Root.5.S45 Root.52.S48 Root.53.S58 Root.6.S55
[53] Root.7.S65 Root.8.S75
<0 rows> (or 0-length row.names)
Thanks
Yogesh
On Sun, Jun 23, 2019 at 3:34 PM Rui Barradas
<ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>> wrote:
Hello,
Please always cc the list.
The data you have posted has the values you want to match as
*row.names*, not as the first column values.
This is why it is important to follow the posting guide and
post
datasets as it suggests, in dput() format.
dput(head(data)) # post the output of this
In the mean time, try
i <- row.names(data) %in% otu.list
data[i, ]
Also, dim(i) doesn't make sense, it's a vector and in R it's
not
expected to have a dim attribute. What would have made sense
would have
been
length(i)
sum(i)
Hope this helps,
Rui Barradas
Às 11:41 de 23/06/19, Yogesh Gupta escreveu:
> Hi Rui,
>
> I used the code as you suggested , it is not giving the
row values, only
> showing the header of rows.
>
>> head(data)
>
> Root-1.S35.L001
Root-10.S75.L001
>
> 71f84e7910006f22684121564206e8ca 0.00000000
0
>
> 03b167b9f86f2519b4263b4125377eed 0.00000000
0
>
> 54e204fb99c80764e964456dadd6a0e5 0.00000000
0
>
> 55cd1fc570879d645bbf7a3642e9b0a8 0.00000000
0
>
> 65f5c31e12c277aec319e2096463f9d2 0.00000000
0
>
> 7bed62f0fef250fd831dcf13bf43f4fc 0.04679457
0
>
>
> .....................................................
>
>
>> head(otu.list)
>
> 9d94ce7d60e59034941e3a12bc37865e
>
> 1 8e60d301122d7aa359eb6b0b00f37f62
>
> 2 bfad6370d28182cc6304844e9bec7fb6
>
> 3 088571139af8e0a63fb6652df8a7438b
>
> 4 ccd70d57890f276a542ef4b5e5142d4c
>
> 5 cab4ca278af34bf722e0c7cb3219370b
>
> 6 72f30f3780145f16ac882eb8e2d189a5
>
>
> ....................................
>
>
>> i <- data[[1]] %in% otu.list
>
>> dim(i)
>
> NULL
>
>> data[i, ]
>
> [1] Root-1.S35.L001 Root-10.S75.L001 Root-13.S5.L001
Root-14.S16.L001
>
> [5] Root-17.S26.L001 Root-18.S36.L001 Root-19.S46.L001
Root-22.S56.L001
>
> [9] Root-24.S66.L001 Root-25.S76.L001 Root-26.S6.L001
Root-27.S17.L001
>
> [13] Root-3.S45.L001 Root-30.S27.L001 Root-32.S37.L001
Root-34.S47.L001
>
> [17] Root-39.S57.L001 Root-4.S55.L001 Root-40.S67.L001
Root-41.S77.L001
>
> [21] Root-43.S7.L001 Root-45.S18.L001 Root-47.S28.L001
Root-50.S38.L001
>
>
> .............
>
>
> Could you please suggest how I can get the row values
along with the harder?
>
>
> Kind Regards
>
> Yogesh
>
>
>
>
> *Yogesh Gupta*
> *Research Fellow*
> *Institute for Global Food Security*
> *Queen's University*
> *Belfast, UK*
>
>
>
> On Fri, Jun 21, 2019 at 9:29 PM Rui Barradas
<ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> <mailto:ruipbarra...@sapo.pt
<mailto:ruipbarra...@sapo.pt>>> wrote:
>
> Hello,
>
> Please don't post in HTML like the posting guide asks
you to, the data
> is unreadable.
>
> Not tested:
>
> i <- data[[1]] %in% ID.list
> data[i, ]
>
>
> That's it.
>
> Hope this helps,
>
> Rui Barradas
>
> Às 21:09 de 21/06/19, Yogesh Gupta escreveu:
> > Hi,
> >
> > I do need to filter data based on first column
could you please
> suggest ,
> > How I can do it in R.
> >
> >
> >
> >
> >
> >
> >
> > head(data)
> >
> >
> >
> > Root-1.S35.L001 Root-10.S75.L001 Root-13.S5.L001
Root-14.S16.L001
> > Root-17.S26.L001
> > 719e20e1e3d19fbc5dd50844c6d29a8f 0.049304262 0 0 0
0.033765858
> > bfffa74c0971b30ccf3b19f65911801f 0 0 0.017210717 0 0
> > 80087a003188288a9b0e3990d72113e3 0 0 0 0.010248632 0
> > aed34f36d535976c247278bec289fd12 0.580694642
0.113445793 0.56221674
> > 0.06764097 0.525782644
> > 42df8f30203380e9a604cb5c4000411b 0 0 0 0.004099453 0
> > d47199c9d9c5417c7cb82ff4159cf497 0 0.019729703 0 0 0
> > 6272cdc38bd517a77ba3887619c36b9f 0 0 0 0.016397811
0.019294776
> > 62a5c6f5e0adda662739a7ac521ea790 0.076695519 0
0.271546861
> 0.254166069
> > 0.463074623
> > 3b5d8860f6a03668df80d364e9591bab 0.125999781
0.019729703 0.061193659
> > 0.038944801 0.02411847
> >
> > I need to extract data for the below IDs
> >
> > head(ID.list)
> >
> > 719e20e1e3d19fbc5dd50844c6d29a8f
> > bfffa74c0971b30ccf3b19f65911801f
> > 62a5c6f5e0adda662739a7ac521ea790
> >
> > I will be tankful for your help.
> >
> > Thanks
> > Yogesh
> >
> > *Yogesh Gupta*
> > *Research Fellow*
> > *Institute for Global Food Security*
> > *Queen's University*
> > *Belfast, UK*
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org <mailto:R-help@r-project.org>
<mailto:R-help@r-project.org <mailto: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.
> >
>
