User: evelyn

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evelyn30
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4 days, 11 hours ago
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6 months, 3 weeks ago
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Posts by evelyn

<prev • 82 results • page 1 of 9 • next >
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Comment: C: R error: vector memory exhausted
... Oh yes, it worked. Thank you so much! ...
written 5 days ago by evelyn30
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Comment: 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 evelyn30
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Comment: 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 evelyn30
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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 evelyn30
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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 evelyn30
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R error: vector memory exhausted
... 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 ...
R written 6 days ago by evelyn30 • updated 6 days ago by Friederike5.1k
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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 evelyn30
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scatter plot for DAPC
... 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 ...
snp written 7 days ago by evelyn30
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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 evelyn30
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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 evelyn30

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Scholar 8 weeks ago, created an answer that has been accepted. For C: Fastq to BAM

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