It seems that Dawn could really benefit from spending some time with
an online R tutorial or two, as she appears not to have much of a clue
about R's basic data structures.
Cheers,
Bert
Bert Gunter
"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
-- Clifford Stoll
On Tue, Jul 14, 2015 at 4:36 PM, Jeff Newmiller
<jdnew...@dcn.davis.ca.us> wrote:
> Well it is pretty obvious that all of your columns have non-numeric data in
> them, but you are the only one who can tell which ones should have been
> numeric, and you are also the one who can peruse your data file in a text
> editor.
> ---------------------------------------------------------------------------
> Jeff Newmiller The ..... ..... Go Live...
> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
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> Research Engineer (Solar/Batteries O.O#. #.O#. with
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> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On July 14, 2015 4:05:37 PM PDT, Dawn <dawn1...@gmail.com> wrote:
>>I used two rows to test the data frame, as follows.
>>
>>> dat <- read.table("TOV_43_Protein_Clusters_abundance1.tab",
>>header=TRUE,sep = "\t")
>>> dat1 <- dat[1:2,]
>>> str(dat1)
>>'data.frame': 2 obs. of 44 variables:
>>$ X : Factor w/ 1075762 levels "","POV_Cluster_1000001",..: 305266
>>625028
>> $ X109DCM: Factor w/ 46 levels "","1","10","109DCM",..: 1 1
>> $ X109SUR: Factor w/ 41 levels "","1","10","109SUR",..: 1 1
>> $ X18DCM : Factor w/ 31 levels "","1","10","11",..: 1 1
>> $ X18SUR : Factor w/ 25 levels "","1","10","11",..: 1 1
>> $ X22SUR : Factor w/ 50 levels "","1","10","11",..: 1 2
>> $ X23DCM : Factor w/ 46 levels "","1","10","11",..: 1 1
>> $ X25DCM : Factor w/ 42 levels "","1","10","11",..: 1 1
>> $ X25SUR : Factor w/ 47 levels "","1","10","11",..: 1 1
>> $ X30DCM : Factor w/ 34 levels "","1","10","11",..: 1 1
>> $ X31SUR : Factor w/ 43 levels "","1","10","11",..: 1 1
>> $ X32DCM : Factor w/ 15 levels "","1","10","11",..: 1 1
>> $ X32SUR : Factor w/ 58 levels "","1","10","11",..: 1 1
>> $ X34DCM : Factor w/ 53 levels "","1","10","11",..: 1 35
>> $ X34SUR : Factor w/ 47 levels "","1","10","11",..: 10 14
>> $ X36DCM : Factor w/ 48 levels "","1","10","11",..: 2 43
>> $ X36SUR : Factor w/ 45 levels "","1","10","11",..: 23 38
>> $ X38DCM : Factor w/ 40 levels "","1","10","11",..: 3 23
>> $ X38SUR : Factor w/ 44 levels "","1","10","11",..: 7 41
>> $ X39DCM : Factor w/ 38 levels "","1","10","11",..: 34 38
>> $ X39SUR : Factor w/ 40 levels "","1","10","11",..: 13 40
>> $ X41DCM : Factor w/ 47 levels "","1","10","11",..: 13 40
>> $ X41SUR : Factor w/ 40 levels "","1","10","11",..: 1 1
>> $ X42DCM : Factor w/ 48 levels "","1","10","11",..: 2 3
>> $ X42SUR : Factor w/ 41 levels "","1","10","11",..: 2 1
>> $ X46SUR : Factor w/ 31 levels "","1","10","11",..: 2 2
>> $ X52DCM : Factor w/ 49 levels "","1","10","11",..: 13 23
>> $ X64DCM : Factor w/ 35 levels "","1","10","11",..: 1 2
>> $ X64SUR : Factor w/ 36 levels "","1","10","11",..: 1 1
>> $ X65DCM : Factor w/ 38 levels "","1","10","11",..: 1 1
>> $ X65SUR : Factor w/ 35 levels "","1","10","11",..: 1 1
>> $ X66DCM : Factor w/ 27 levels "","1","10","11",..: 1 1
>> $ X66SUR : Factor w/ 35 levels "","1","10","11",..: 1 1
>> $ X67SUR : Factor w/ 38 levels "","1","10","11",..: 1 1
>> $ X68DCM : Factor w/ 33 levels "","1","10","11",..: 1 1
>> $ X68SUR : Factor w/ 36 levels "","1","10","11",..: 1 1
>> $ X70MES : Factor w/ 23 levels "","1","10","11",..: 1 1
>> $ X70SUR : Factor w/ 37 levels "","1","10","11",..: 1 1
>> $ X72DCM : Factor w/ 40 levels "","1","10","11",..: 13 27
>> $ X72SUR : Factor w/ 38 levels "","1","10","11",..: 1 1
>> $ X76DCM : Factor w/ 44 levels "","1","10","11",..: 1 1
>> $ X76SUR : Factor w/ 34 levels "","1","10","11",..: 1 1
>> $ X82DCM : Factor w/ 29 levels "","1","10","11",..: 1 1
>> $ X85DCM : Factor w/ 30 levels "","1","10","11",..: 1 1
>>
>>
>>Thank you!!
>>Dawn
>>
>>On Tue, Jul 14, 2015 at 3:48 PM, Jeff Newmiller
>><jdnew...@dcn.davis.ca.us>
>>wrote:
>>
>>> I suspect your data frame "dat" has non-numeric data in some of the
>>> columns that have ABC in their names. Any column of a data frame can
>>be
>>> numeric or not, but the data frame as a unit cannot be numeric. If
>>your
>>> data file has odd characters in done of the otherwise-numeric
>>columns, the
>>> whole column will be read in as a factor or character strings. Look
>>at the
>>> output of str(dat) for columns that don't show "num'. If you can find
>>the
>>> column, and then one of the bad rows, you can use a text editor to
>>fix them
>>> manually, or show us examples of the bad data and we can suggest ways
>>to
>>> fix it in R.
>>>
>>---------------------------------------------------------------------------
>>> Jeff Newmiller The ..... ..... Go
>>Live...
>>> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live
>>> Go...
>>> Live: OO#.. Dead: OO#..
>>Playing
>>> Research Engineer (Solar/Batteries O.O#. #.O#. with
>>> /Software/Embedded Controllers) .OO#. .OO#.
>>rocks...1k
>>>
>>---------------------------------------------------------------------------
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On July 14, 2015 2:35:38 PM PDT, Dawn <dawn1...@gmail.com> wrote:
>>> >Hi,
>>> >
>>> >I used a small set of data (several columns and rows) and it works
>>fine
>>> >using the following command:
>>> >abc <- rowSums(test[,grep("ABC",names(test),fixed=T)],na.rm=T)
>>> >
>>> >But when I used the real big data table, "Error in rowSums(dat[,
>>> >grep("ABC", names(dat), fixed = T)], na.rm = T) :
>>> > 'x' must be numeric"
>>> >Then it didn't work either using as.numeric():
>>> >> as.numeric(dat)
>>> >Error: (list) object cannot be coerced to type 'double'
>>> >
>>> >Thanks!
>>> >Dawn
>>> >
>>> >
>>> >
>>> >
>>> >On Fri, Jul 10, 2015 at 4:35 PM, Dawn <dawn1...@gmail.com> wrote:
>>> >
>>> >> Thank you all and sorry for the data messing. It has worked!
>>> >>
>>> >> Best,
>>> >> Dawn
>>> >>
>>> >> On Fri, Jul 10, 2015 at 4:15 AM, Jim Lemon <drjimle...@gmail.com>
>>> >wrote:
>>> >>
>>> >>> Hi Dawn,
>>> >>> Your data are a bit messed up, but try the following:
>>> >>>
>>> >>> colSums(dat[,grep("ABC",names(dat),fixed=TRUE)],na.rm=TRUE)
>>> >>> colSums(dat[,grep("XYZ",names(dat),fixed=TRUE)],na.rm=TRUE)
>>> >>>
>>> >>> I'm assuming that you want to discard the NA values.
>>> >>>
>>> >>> Jim
>>> >>>
>>> >>> On Fri, Jul 10, 2015 at 6:52 AM, Rui Barradas
>><ruipbarra...@sapo.pt>
>>> >>> wrote:
>>> >>> > Hello,
>>> >>> >
>>> >>> > Please use ?dput to give a data example, like this it's
>>completely
>>> >>> > unreadable. If your data.frame is named 'dat' use
>>> >>> >
>>> >>> > dput(head(dat, 30)) # paste the outut of this in your mail
>>> >>> >
>>> >>> >
>>> >>> > And don't post in html, use plain text only, like the posting
>>> >guide
>>> >>> says.
>>> >>> >
>>> >>> > Rui Barradas
>>> >>> >
>>> >>> >
>>> >>> > Em 09-07-2015 18:12, Dawn escreveu:
>>> >>> >>
>>> >>> >> Hi,
>>> >>> >>
>>> >>> >> I have a big dataframe as follows
>>> >>> >>
>>> >>> >> 109ABC 109XYZ 18ABC 18XYZ 22XYZ 23ABC
>>> >25ABC
>>> >>> >> 25XYZ
>>> >>> >> 30ABC 31XYZ 32ABC 32XYZ 34DCM 34XYZ
>>36ABC
>>> >>> 36SUR
>>> >>> >> 38DCM 38XYZ 39DCM 39SUR 41DCM 41SUR 42DCM
>>> >42SUR
>>> >>> >> 46SUR 52DCM 64ABC 64XYZ 65ABC 65XYZ 66ABC
>>> >66XYZ
>>> >>> >> 67XYZ 68ABC 68SUR 70MES 70SUR 72ABC 72XYZ
>>> >76ABC
>>> >>> >> 76XYZ 82ABC 85ABC POV
>>> >>> >> Cluster_1
>>> >17
>>> >>> 1
>>> >>> >> 3 10 14 5 2 2 1 1 1 2
>>> >>> >> 2 TT:61
>>> >>> >> Cluster_2 1
>>4
>>> > 20
>>> >>> >> 6 5 3 6 9 9 6 10 1 3 1
>>> >>> >> 4
>>TT:88
>>> >>> >> Cluster_3 3 3 6 4
>>> > 17
>>> >>> >> 17 18 13 17 19 22 11 5 21 8 5
>>18
>>> > 4
>>> >>> >> 7 9
>>> >>> >> TT:227
>>> >>> >> ........
>>> >>> >>
>>> >>> >> I want to get two columns, i.e, one is to sum columns for all
>>> >>> including
>>> >>> >> ABC for each row and the other is to sum columns for all
>>> >including XYZ
>>> >>> >> for
>>> >>> >> each row.
>>> >>> >>
>>> >>> >> Is there some help? Thank you!
>>> >>> >> Dawn
>>> >>> >>
>>> >>> >> [[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.
>>> >>> >>
>>> >>> >
>>> >>> > ______________________________________________
>>> >>> > 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.
>>> >>>
>>> >>
>>> >>
>>>
>>>
>
> ______________________________________________
> 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.
______________________________________________
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.
