User: evelyn
evelyn • 30
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Posts by evelyn
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C: R error: vector memory exhausted
... Oh yes, it worked. Thank you so much! ...
written 5 days ago by
evelyn • 30
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C: R error: vector memory exhausted
... Thank you, @Friederike! I have tried your awk statement and it filters out the '`NA's`. But I have a confusion about how it filters:
'$1 < 0.95' resulted in 35736361 lines
'$1 < 0.90' resulted in 17351161 lines
'$1 < 0.80' resulted in 7030538 lines
However, `'$1 < 0.95' ...
written 6 days ago by
evelyn • 30
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C: R error: vector memory exhausted
... Thank you, @Sam! The first issue I had with my data file was its big size. R freezes or aborts if I try to import the file directly. That's why I split it into the smaller parts and combined later after filtering. ...
written 6 days ago by
evelyn • 30
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Comment:
C: R error: vector memory exhausted
... I apologize for any confusion. I am using an input text file (merged vcf from multiple samples). For illustration, I kept four samples here. A few lines from the original input file which has a size of 35 GB looks like:
Sample_1 Sample_2 Sample_3 Sample_4
NA NA NA NA
A A T G
T T T T ...
written 6 days ago by
evelyn • 30
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Comment:
C: R error: vector memory exhausted
... Once RData files are made, I filter those for missing and redundant markers using:
library(data.table)
all <- NULL
for(i in 1:50){
load(paste0("input",i,".RData"))
df <- unique(df)
count.nas <- rowSums(is.na(df))
df<-df[-which(count.nas>(0.10*ncol( ...
written 6 days ago by
evelyn • 30
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... I split a large vcf file with multiple samples to small vcf.gz files using a loop. I am trying to convert these small vcf.gz files to RData files using a loop but I get an error of vector memory loss. The original file is 35 GB in size. The code works well for an original file of size 28 GB. I am us ...
written 6 days ago by
evelyn • 30
• updated
6 days ago by
Friederike ♦ 5.1k
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Comment:
C: scatter plot for DAPC
... For results, I am getting the center boxes. I have found an example [here][1] similar to what I am getting. I think customization will work to modify the data points. But in my case, there are no data points shown.
[1]: https://www.google.com/imgres?imgurl=x-raw-image%3A%2F%2F%2Fce27563b01b ...
written 7 days ago by
evelyn • 30
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... I am doing DAPC for SNP dataset using:
library(adegenet)
x<-input_file
x1<-as.data.frame(t(x))
gen<-as.genlight(x1)
grp<-find.clusters(gen,max.n.clust = 10)
dapc1<-dapc(gen,grp$grp)
scatter(dapc1)
But the scatter plot shows clusters without the individua ...
written 7 days ago by
evelyn • 30
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Comment:
C: snp filtering for text file
... So `rbindlist` can not work with RData format? I could not find an easy way to convert `RData` to `data.frame`. ...
written 12 days ago by
evelyn • 30
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Comment:
C: snp filtering for text file
... Thank you, @zx8754! I tried using your code. It filters the markers but gives an error at the end:
Error in rbindlist(lapply(1:40, function(i) { :
Item 1 of input is not a data.frame, data.table or list
My input files for the loop are `RData` files. ...
written 13 days ago by
evelyn • 30
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