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> 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> 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>
>> 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>> 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> 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]]
______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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