Thanks so much for this. Unfortunately, cbind did not work. Basically, I like to put an extra column named "chr" in the combined file from 22 chr. So chr colum will be "1" for the portion of chr1 in the combined file, 2 for the portion of chr2 in the combined file and so on. Regards, Greg On Thu, Feb 2, 2017 at 9:39 AM, Rui Barradas <ruipbarradas at sapo.pt> wrote:> Hello, > > If I understand correctly, just use ?cbind. > > Rui Barradas > > Em 02-02-2017 13:33, greg holly escreveu: > >> Hi Rui; >> >> Is there any way to insert the chr ids in numeric as 1,2......,22 in the >> final output. Here is output from str(temp). So I need also chr ids in a >> column. >> 1 rs58108140 10583 G A -0.070438 0.059903 >> 2 rs189107123 10611 C G -0.044916 0.085853 >> >> Regards, >> Greg >> >> >> On Wed, Feb 1, 2017 at 1:32 PM, Rui Barradas <ruipbarradas at sapo.pt >> <mailto:ruipbarradas at sapo.pt>> wrote: >> >> Hello, >> >> If what you want is to combine the files into one data.frame then >> there are 2 things you should see: >> >> 1) You create a variable named 'temp' and don't ever use it. >> 2) You never combine the data.frames you read in. >> >> Try instead the following. >> >> temp <- data.frame() >> for(i in 1:22) { >> infile<-paste("chr",i,"/Z-score.imputed",sep="") >> psT<-read.table(infile,header=T,as.is <http://as.is>=T,sep="\t") >> temp <- rbind(temp, psT) >> } >> >> str(temp) # to see what you have >> >> Hope this helps, >> >> Rui Barradas >> >> >> >> >> Em 01-02-2017 17:25, greg holly escreveu: >> >> Hi all; >> >> I have 22 directories named chr1, chr2,....,chr22. Each >> directory has a >> file named "Z-score.imputed". I would like to combine >> Z-score.imputed >> files into one. I wrote the following loop but did not get any >> results. >> Your helps are highly appreciated. >> >> regards, >> >> Greg >> >> temp<-c() >> >> for(i in 1:22) { >> infile<-paste("chr",i,"/Z-score.imputed",sep="") >> psT<-read.table(as.character(infile),header=T,as.is >> <http://as.is>=T,sep="\t") >> ps<-psT[psT$Var>0.6,] >> ratio=nrow(ps)/nrow(psT) >> print(ratio) >> } >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list >> -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> <https://stat.ethz.ch/mailman/listinfo/r-help> >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> <http://www.R-project.org/posting-guide.html> >> and provide commented, minimal, self-contained, reproducible code. >> >> >>[[alternative HTML version deleted]]
Hi. Your messages are rather confusing. Well, if you could get correct final data.frame in loop why not just add inside of loop new column(s) by psT$chr <- i Maybe it is time to read R intro as good source for starting with R. It has about 100 pages, but you can pick as start only pages 2-40 which are basic for data input and manipulation. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg holly > Sent: Thursday, February 2, 2017 4:13 PM > To: Rui Barradas <ruipbarradas at sapo.pt> > Cc: r-help mailing list <r-help at r-project.org> > Subject: Re: [R] looping problem > > Thanks so much for this. Unfortunately, cbind did not work. Basically, I like to > put an extra column named "chr" in the combined file from 22 chr. > So chr colum will be "1" for the portion of chr1 in the combined file, 2 for the > portion of chr2 in the combined file and so on. > > Regards, > > Greg > > On Thu, Feb 2, 2017 at 9:39 AM, Rui Barradas <ruipbarradas at sapo.pt> wrote: > > > Hello, > > > > If I understand correctly, just use ?cbind. > > > > Rui Barradas > > > > Em 02-02-2017 13:33, greg holly escreveu: > > > >> Hi Rui; > >> > >> Is there any way to insert the chr ids in numeric as 1,2......,22 in > >> the final output. Here is output from str(temp). So I need also chr > >> ids in a column. > >> 1 rs58108140 10583 G A -0.070438 0.059903 > >> 2 rs189107123 10611 C G -0.044916 0.085853 > >> > >> Regards, > >> Greg > >> > >> > >> On Wed, Feb 1, 2017 at 1:32 PM, Rui Barradas <ruipbarradas at sapo.pt > >> <mailto:ruipbarradas at sapo.pt>> wrote: > >> > >> Hello, > >> > >> If what you want is to combine the files into one data.frame then > >> there are 2 things you should see: > >> > >> 1) You create a variable named 'temp' and don't ever use it. > >> 2) You never combine the data.frames you read in. > >> > >> Try instead the following. > >> > >> temp <- data.frame() > >> for(i in 1:22) { > >> infile<-paste("chr",i,"/Z-score.imputed",sep="") > >> psT<-read.table(infile,header=T,as.is <http://as.is>=T,sep="\t") > >> temp <- rbind(temp, psT) > >> } > >> > >> str(temp) # to see what you have > >> > >> Hope this helps, > >> > >> Rui Barradas > >> > >> > >> > >> > >> Em 01-02-2017 17:25, greg holly escreveu: > >> > >> Hi all; > >> > >> I have 22 directories named chr1, chr2,....,chr22. Each > >> directory has a > >> file named "Z-score.imputed". I would like to combine > >> Z-score.imputed > >> files into one. I wrote the following loop but did not get any > >> results. > >> Your helps are highly appreciated. > >> > >> regards, > >> > >> Greg > >> > >> temp<-c() > >> > >> for(i in 1:22) { > >> infile<-paste("chr",i,"/Z-score.imputed",sep="") > >> psT<-read.table(as.character(infile),header=T,as.is > >> <http://as.is>=T,sep="\t") > >> ps<-psT[psT$Var>0.6,] > >> ratio=nrow(ps)/nrow(psT) > >> print(ratio) > >> } > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help at r-project.org <mailto:R-help at r-project.org> mailing list > >> -- To UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> <https://stat.ethz.ch/mailman/listinfo/r-help> > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> <http://www.R-project.org/posting-guide.html> > >> and provide commented, minimal, self-contained, reproducible code. > >> > >> > >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. 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Thanks so much Peter. I do appreciate for this. Greg On Thu, Feb 2, 2017 at 10:28 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi. > > Your messages are rather confusing. Well, if you could get correct final > data.frame in loop why not just add inside of loop new column(s) by > > psT$chr <- i > > Maybe it is time to read R intro as good source for starting with R. It > has about 100 pages, but you can pick as start only pages 2-40 which are > basic for data input and manipulation. > > Cheers > Petr > > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 2, 2017 4:13 PM > > To: Rui Barradas <ruipbarradas at sapo.pt> > > Cc: r-help mailing list <r-help at r-project.org> > > Subject: Re: [R] looping problem > > > > Thanks so much for this. Unfortunately, cbind did not work. Basically, I > like to > > put an extra column named "chr" in the combined file from 22 chr. > > So chr colum will be "1" for the portion of chr1 in the combined file, 2 > for the > > portion of chr2 in the combined file and so on. > > > > Regards, > > > > Greg > > > > On Thu, Feb 2, 2017 at 9:39 AM, Rui Barradas <ruipbarradas at sapo.pt> > wrote: > > > > > Hello, > > > > > > If I understand correctly, just use ?cbind. > > > > > > Rui Barradas > > > > > > Em 02-02-2017 13:33, greg holly escreveu: > > > > > >> Hi Rui; > > >> > > >> Is there any way to insert the chr ids in numeric as 1,2......,22 in > > >> the final output. Here is output from str(temp). So I need also chr > > >> ids in a column. > > >> 1 rs58108140 10583 G A -0.070438 0.059903 > > >> 2 rs189107123 10611 C G -0.044916 0.085853 > > >> > > >> Regards, > > >> Greg > > >> > > >> > > >> On Wed, Feb 1, 2017 at 1:32 PM, Rui Barradas <ruipbarradas at sapo.pt > > >> <mailto:ruipbarradas at sapo.pt>> wrote: > > >> > > >> Hello, > > >> > > >> If what you want is to combine the files into one data.frame then > > >> there are 2 things you should see: > > >> > > >> 1) You create a variable named 'temp' and don't ever use it. > > >> 2) You never combine the data.frames you read in. > > >> > > >> Try instead the following. > > >> > > >> temp <- data.frame() > > >> for(i in 1:22) { > > >> infile<-paste("chr",i,"/Z-score.imputed",sep="") > > >> psT<-read.table(infile,header=T,as.is <http://as.is > >=T,sep="\t") > > >> temp <- rbind(temp, psT) > > >> } > > >> > > >> str(temp) # to see what you have > > >> > > >> Hope this helps, > > >> > > >> Rui Barradas > > >> > > >> > > >> > > >> > > >> Em 01-02-2017 17:25, greg holly escreveu: > > >> > > >> Hi all; > > >> > > >> I have 22 directories named chr1, chr2,....,chr22. Each > > >> directory has a > > >> file named "Z-score.imputed". I would like to combine > > >> Z-score.imputed > > >> files into one. I wrote the following loop but did not get any > > >> results. > > >> Your helps are highly appreciated. > > >> > > >> regards, > > >> > > >> Greg > > >> > > >> temp<-c() > > >> > > >> for(i in 1:22) { > > >> infile<-paste("chr",i,"/Z-score.imputed",sep="") > > >> psT<-read.table(as.character(infile),header=T,as.is > > >> <http://as.is>=T,sep="\t") > > >> ps<-psT[psT$Var>0.6,] > > >> ratio=nrow(ps)/nrow(psT) > > >> print(ratio) > > >> } > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> ______________________________________________ > > >> R-help at r-project.org <mailto:R-help at r-project.org> mailing > list > > >> -- To UNSUBSCRIBE and more, see > > >> https://stat.ethz.ch/mailman/listinfo/r-help > > >> <https://stat.ethz.ch/mailman/listinfo/r-help> > > >> PLEASE do read the posting guide > > >> http://www.R-project.org/posting-guide.html > > >> <http://www.R-project.org/posting-guide.html> > > >> and provide commented, minimal, self-contained, reproducible > code. > > >> > > >> > > >> > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at 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. > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. >[[alternative HTML version deleted]]