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.pi...@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-boun...@r-project.org] On Behalf Of Bogdan > > Tanasa > > Sent: Monday, July 3, 2017 9:22 AM > > To: r-help <r-help@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@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 jakékoliv k němu připojené dokumenty jsou důvěrné a jsou > určeny pouze jeho adresátům. > Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě > neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie > vymažte ze svého systému. > Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email > jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. > Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi > či zpožděním přenosu e-mailu. > > V případě, že je tento e-mail součástí obchodního jednání: > - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření > smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. > - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; > Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany > příjemce s dodatkem či odchylkou. > - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve > výslovným dosažením shody na všech jejích náležitostech. > - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za > společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn > nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto > emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich > existence je adresátovi či osobě jím zastoupené známá. > > 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]] ______________________________________________ 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.
