I attached the file including the first two rows and please help to make it
the numeric data frame. Hopefully the following command works:
dcm <- rowSums(dat1[,grep("DCM",names(dat1),fixed=T)],na.rm=T)
Thank you very much!
Dawn
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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> ---------------------------------------------------------------------------
> 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.
> >> >>>
> >> >>
> >> >>
> >>
> >>
>
>
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