User: aleix.arnau1990

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Posts by aleix.arnau1990

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Software to perform GxE iGWAS for a binary disease with a quantitative E factor.
... Hi! Does someone know what is the best way or software to perform GxE iGWAS for qualitative traits using a quantitative variable as Environment? I know plink is able to perform GxE iGWAS for quantitative traits with binary environment variables. But not further than that. Is there someone with exper ...
igwas written 4.6 years ago by aleix.arnau199010
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Comment: C: QQ plot - how to add gris shadow showing confidence interval
... Don't worry! I found GWASTools package from bioconductor which solved my problem. Thanks for all. ...
written 4.6 years ago by aleix.arnau199010
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Comment: C: QQ plot - how to add gris shadow showing confidence interval
...   Thanks Ahill! But now, with my code like this: assoc<-read.table("all_SNPs_assoc.txt",header=TRUE,dec=".") png("QQplot.png") P<-assoc_allSNPs_mperm$P qq.chisq(-2 * log(P), df = 2, conc=c(0.05, 0.95)) abline(0,1) dev.off() It provides a nice plot, but with x and y axis in chi-squared valu ...
written 4.6 years ago by aleix.arnau199010
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QQ plot - how to add gris shadow showing confidence interval
...   Hi! I am trying to plot a QQplot with results from a gwas runned with plink. I would like to know how can I add the tipical grey shadow showing confidence interval (95%CI). I can not find it. Does someone know? My plot looks like that: assoc<-read.table("all_SNPs_assoc.txt",header=TRUE,dec= ...
R qqplot written 4.6 years ago by aleix.arnau199010 • updated 4.6 years ago by PoGibas4.8k
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Comment: C: What is the definition of LOC# identifier?
... I think you post your answer in a wrong place. ...
written 4.6 years ago by aleix.arnau199010
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What is the definition of LOC# identifier?
... Hi, Could someone give me the definition of LOC# identifiers and where can I found it? I cannot find any place with the criteria to give to a gene an identifier such as LOC#. Thanks!   ...
anotation genesymbol written 4.6 years ago by aleix.arnau199010 • updated 4.5 years ago by Giovanni M Dall'Olio26k
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Convert Rat to Human region cordinates
... Dear all,   I have regions from a human genome and I want to get the equivalent regions in rat genome. I saw a paper which use galaxy to do it but the lift-over convert genome coordinates tool doesn't work (I don't know why). My data looks like this: #chr     #start_position   #end_position 1   ...
galaxy written 4.6 years ago by aleix.arnau199010 • updated 4.6 years ago by PoGibas4.8k
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Set-based test - PLINK
... Hi, Plink documentation explains two options when running a set-based test analysis. HINT Two extremes are to perform a test based on a) the best single SNP result per set:  --set-max 1 --set-p 1 or to use all SNPs in a set: --set-max 99999 --set-p 1 --set-r2 1 Could someone tell me what a ...
plink written 4.7 years ago by aleix.arnau199010 • updated 3.9 years ago by christopher medway440
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RepeatExplorer from Galaxy
... Hi, I've been using RepeatExplorer from Galaxy Environment to characterize repeat elements from the genus Begonia.s I'm looking for someone who has used that before or known well this tool. What I need is how can I get the "consensus sequence" from each cluster. I mean, Repeat Explorer provides clu ...
repeatexplorer repeat elements written 5.5 years ago by aleix.arnau199010 • updated 5.5 years ago by SES8.2k
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Find Genome Source From A Blast.
... Hi, I've made a blast with the sequences from a plant's transcriptome which don't match to our genome. We want to know where they come from to try to improve our genome. The problem is that I have thousands of sequences, so, thousands of blast results. So, the question is if there are someone who kn ...
bioconductor blastn blast written 5.7 years ago by aleix.arnau199010

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