[adegenet-forum] genind object too big for sPCA?

[Roman Luštrik]

Can you check the memory usage? Is it consuming all the RAM? If not, they it's probably not a memory issue and the culprit is somewhere else. Have you tried running the analysis on a subset of data? 

Cheers, 
Roman 


---- 
In god we trust, all others bring data. 
> Zahtevaj IJZ na https://kurc.biolitika.si 


From: "Judy (Duffie), Caroline" <JudyC at si.edu> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Wednesday, November 8, 2017 7:06:05 PM 
Subject: Re: [adegenet-forum] genind object too big for sPCA? 

Update - I tried running the same script on a computer with 64 GB of memory. Same issues. 




On Nov 7, 2017, at 12:13 PM, Judy (Duffie), Caroline < JudyC at si.edu > wrote: 

Hi all, 

I’m having trouble running an sPCA on a genind object (10.6Mb) that contains about 160 individuals and 6500 SNPs - When I run the command: 'mySpca <- spca(data, ask=FALSE, type=1, scannf=FALSE)” R crashes - i.e. I get the “whirling ball of death” and the program becomes unresponsive. 

I’ve seen some older messages on the forum that similarly report problems with larger genind objects, but responses indicate that there shouldn’t be a memory issue ( http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2012-June/000513.html ). I’m running on a MBP with 16 GB of memory. 

Any tips or tricks for running an object of this size? Interestingly I’ve been able to run a PCA and DAPC without issue. 

#Convert structure file to a genind object. 
> data <- read.structure("~/Documents/Trochilus/second_chapter/Analysis/structure/input/GBS_all_pop_pheno.stru", 
+ n.ind=158, 
+ n.loc=6451, 
+ onerowperin=TRUE, 
+ col.lab=1, 
+ col.pop=2, 
+ col.others=3:8, 
+ row.marknames=0, 
+ ask=FALSE, 
+ ) 

Converting data from a STRUCTURE .stru file to a genind object... 

> #add xy data as a separate element in the list $other 
> other(data)$xy <- other(data)$X[, 5:6] 
> mode(other(data)$xy) <- "numeric" 
> colnames(other(data)$xy) <- c("x", "y") 
> #define strata 
> strata(data) <- as.data.frame(other(data)$X[, 1:3]) 
> nameStrata(data) <-c("sex","phenotype", "HI") 
> 
> # add jitter 
> data$other$xy <-jitter(data$other$xy, factor = 1, amount = NULL) 

> mySpca <- spca(data, ask=FALSE, type=1, scannf=FALSE) 


Caroline D. Judy 
PhD Candidate (LSU) 
Peter Buck Predoctoral Fellow (NMNH) 
email: judyc at si.edu 







Caroline D. Judy 
PhD Candidate (LSU) 
Peter Buck Predoctoral Fellow (NMNH) 
email: judyc at si.edu 




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