Jack Arnestad
2018-Apr-21 19:16 UTC
[R] Removing columns from big.matrix which have only one value
I have a very large binary matrix, stored as a big.matrix to conserve memory (it is over 2 gb otherwise - 5 million columns and 100 rows). r <- 100 c <- 10000 m4 <- matrix(sample(0:1,r*c, replace=TRUE),r,c) m4 <- cbind(m4, 1) m4 <- as.big.matrix(m4) I need to remove every column which has only one unique value (in this case, only 0s or only 1s). Because of the number of columns, I want to be able to do this in parallel. How can I accomplish this while keeping the data compressed as a big.matrix? I can convert it into a df and loop over the columns looking for the number of unique values, but this takes too much RAM. Thanks! [[alternative HTML version deleted]]
Bert Gunter
2018-Apr-21 20:54 UTC
[R] Removing columns from big.matrix which have only one value
Maybe base R's unique() function might be useful? It uses hashing I believe. Bert On Sat, Apr 21, 2018, 12:17 PM Jack Arnestad <jackarnestad at gmail.com> wrote:> I have a very large binary matrix, stored as a big.matrix to conserve > memory (it is over 2 gb otherwise - 5 million columns and 100 rows). > > r <- 100 > c <- 10000 > m4 <- matrix(sample(0:1,r*c, replace=TRUE),r,c) > m4 <- cbind(m4, 1) > m4 <- as.big.matrix(m4) > > I need to remove every column which has only one unique value (in this > case, only 0s or only 1s). Because of the number of columns, I want to be > able to do this in parallel. > > How can I accomplish this while keeping the data compressed as a > big.matrix? I can convert it into a df and loop over the columns looking > for the number of unique values, but this takes too much RAM. > > Thanks! > > [[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. >[[alternative HTML version deleted]]
PIKAL Petr
2018-Apr-23 12:41 UTC
[R] Removing columns from big.matrix which have only one value
Hi With> which(colSums(m4)==0)you get column numbers with only zeroes. You could also remove zero column by. m4[,colSums(m4)!=0] And with that you could find colums with ones. which(colSums(m4)==nrow(m4)) [1] 10001 Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Jack Arnestad > Sent: Saturday, April 21, 2018 9:17 PM > To: r-help at r-project.org > Subject: [R] Removing columns from big.matrix which have only one value > > I have a very large binary matrix, stored as a big.matrix to conserve memory (it > is over 2 gb otherwise - 5 million columns and 100 rows). > > r <- 100 > c <- 10000 > m4 <- matrix(sample(0:1,r*c, replace=TRUE),r,c) > m4 <- cbind(m4, 1) > m4 <- as.big.matrix(m4) > > I need to remove every column which has only one unique value (in this case, > only 0s or only 1s). Because of the number of columns, I want to be able to do > this in parallel. > > How can I accomplish this while keeping the data compressed as a big.matrix? I > can convert it into a df and loop over the columns looking for the number of > unique values, but this takes too much RAM. > > Thanks! > > [[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.