You can also fit a linear model with a matrix-valued response
variable, which should be even faster (not sure off the top of my head
how to get the residuals and reshape them to the dimensions you want)
On Fri, Aug 9, 2024 at 9:31?PM Bert Gunter <bgunter.4567 at gmail.com>
wrote:>
> See ?lm.fit.
> I must be missing something, because:
>
> results <- sapply(74:35164, \(i) residuals(lm.fit(purity2,
> gem751be.rpkm[, i] )))
>
> would give you a 751 x 35091 matrix of the residuals from each of the
> regressions.
> I assume it will be considerably faster than all the overhead you are
> carrying in your current code, but of course you'll have to try it and
> see. ... Assuming that I have interpreted your request correctly.
> Ignore if not.
>
> Cheers,
> Bert
>
> On Fri, Aug 9, 2024 at 4:50?PM Yuan Chun Ding via R-help
> <r-help at r-project.org> wrote:
> >
> > Dear R users,
> >
> > I am running the following code below, the gem751be.rpkm is a
dataframe with dim of 751 samples by 35164 variables, 73 phenotypic variables
in the furst to 73rd column and 35091 genomic variables or genes in the 74th to
35164th columns. What I need to do is to calculate the residuals for each gene
using the simple linear regression model of genelist[i] ~ purity2;
> >
> > The following code is running, it takes long time, but I have an
expensive ThinkStation window computer.
> > Can you provide a fast way to do it?
> >
> > Thank you,
> >
> > Ding
> >
> >
---------------------------------------------------------------------------------
> >
> >
> > gem751be.rpkm <-merge(gem751be10, as.data.frame(t(rna849.fpkm2)),
> > + by.x="id2",by.y=0)
> > > row.names(gem751be.rpkm)<-gem751be.rpkm$id3
> > >
colnames(gem751be.rpkm)<-gsub(colnames(gem751be.rpkm),pattern="-",replacement="_")
> > > genelist <- gem751be.rpkm %>% dplyr::select(74:35164)
> > > residuals <- NULL
> > > for (i in 1:length(genelist)) {
> > + #i=1
> > + formula <- reformulate("purity2",
response=names(genelist)[i])
> > + model <- lm(formula, data = gem751be.rpkm)
> > + resi <- as.data.frame(residuals(model))
> > + colnames(resi)[1]<-names(genelist)[i]
> > + resi <-as.data.frame(t(resi))
> > + residuals <- rbind(residuals, resi)
> > + }
> >
> >
> >
> > ----------------------------------------------------------------------
> > ------------------------------------------------------------
> > -SECURITY/CONFIDENTIALITY WARNING-
> >
> > This message and any attachments are intended solely for the
individual or entity to which they are addressed. This communication may contain
information that is privileged, confidential, or exempt from disclosure under
applicable law (e.g., personal health information, research data, financial
information). Because this e-mail has been sent without encryption, individuals
other than the intended recipient may be able to view the information, forward
it to others or tamper with the information without the knowledge or consent of
the sender. If you are not the intended recipient, or the employee or person
responsible for delivering the message to the intended recipient, any
dissemination, distribution or copying of the communication is strictly
prohibited. If you received the communication in error, please notify the sender
immediately by replying to this message and deleting the message and any
accompanying files from your system. If, due to the security risks, you do not
wish to rec
> > eive further communications via e-mail, please reply to this message
and inform the sender that you do not wish to receive further e-mail from the
sender. (LCP301)
> > ------------------------------------------------------------
> >
> > [[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.
>
> ______________________________________________
> 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.