Dear all, I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ATR INDEL 22M ATR SNV 11M BTK SNV 11M BTK INDEL I would like to transform this DATAFRAME into a MATRIX that has GENE on ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL (ie the types of mutations). The R code starts with : y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type) z <- acast(y, Cancer_Gene ~ Sample) although in z, I do not have the information on Type (i.e.SNV or INDEL). thanks a lot, -- bogdan [[alternative HTML version deleted]]
Hi Bogdan,
If you want something like this:
22M 17M 11M
AEBP1 SNV SNV NA
ATR INDEL NA NA
ATR SNV NA NA
BTK NA NA SNV
BTK NA NA INDEL
You're in trouble with repeated row names. Same with column names if
you add extra columns for repeated values. You'll have to change
something in order to make this consistent.
Jim
On Mon, Jul 3, 2017 at 5:22 PM, Bogdan Tanasa <tanasa at gmail.com>
wrote:> Dear all,
>
> I would appreciate please a piece of help regarding the use of acast/dcast
> functions in reshape2 package.
>
> Specifically, I'm working with a data frame, that has information about
> SAMPLE, GENE, and TYPE of MUTATION (as shown below):
>
> Sample Gene Type
> 22M AEBP1 SNV
> 17M AEBP1 SNV
> 22M ATR INDEL
> 22M ATR SNV
> 11M BTK SNV
> 11M BTK INDEL
>
>
> I would like to transform this DATAFRAME into a MATRIX that has GENE on
> ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL
> (ie the types of mutations).
>
> The R code starts with :
>
> y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type)
>
> z <- acast(y, Cancer_Gene ~ Sample)
>
> although in z, I do not have the information on Type (i.e.SNV or INDEL).
>
> thanks a lot,
>
> -- bogdan
>
> [[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.
Hi Do you want something like dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) or dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) 1 means INDEL, 2 means SNV and three means both Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bogdan > Tanasa > Sent: Monday, July 3, 2017 9:22 AM > To: r-help <r-help at r-project.org> > Subject: [R] reshaping the data > > Dear all, > > I would appreciate please a piece of help regarding the use of acast/dcast > functions in reshape2 package. > > Specifically, I'm working with a data frame, that has information about > SAMPLE, GENE, and TYPE of MUTATION (as shown below): > > Sample Gene Type > 22M AEBP1 SNV > 17M AEBP1 SNV > 22M ATR INDEL > 22M ATR SNV > 11M BTK SNV > 11M BTK INDEL > > > I would like to transform this DATAFRAME into a MATRIX that has GENE on > ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL > (ie the types of mutations). > > The R code starts with : > > y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type) > > z <- acast(y, Cancer_Gene ~ Sample) > > although in z, I do not have the information on Type (i.e.SNV or INDEL). > > thanks a lot, > > -- bogdan > > [[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.
Thanks a lot gentlemen, and particularly Petr -- the R code you did share helped tremendously ;) On Mon, Jul 3, 2017 at 2:53 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi > > Do you want something like > > dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) > > or > > dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) > > 1 means INDEL, 2 means SNV and three means both > > Cheers > Petr > > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bogdan > > Tanasa > > Sent: Monday, July 3, 2017 9:22 AM > > To: r-help <r-help at r-project.org> > > Subject: [R] reshaping the data > > > > Dear all, > > > > I would appreciate please a piece of help regarding the use of > acast/dcast > > functions in reshape2 package. > > > > Specifically, I'm working with a data frame, that has information about > > SAMPLE, GENE, and TYPE of MUTATION (as shown below): > > > > Sample Gene Type > > 22M AEBP1 SNV > > 17M AEBP1 SNV > > 22M ATR INDEL > > 22M ATR SNV > > 11M BTK SNV > > 11M BTK INDEL > > > > > > I would like to transform this DATAFRAME into a MATRIX that has GENE on > > ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL > > (ie the types of mutations). > > > > The R code starts with : > > > > y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type) > > > > z <- acast(y, Cancer_Gene ~ Sample) > > > > although in z, I do not have the information on Type (i.e.SNV or INDEL). > > > > thanks a lot, > > > > -- bogdan > > > > [[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]]