User: Sam

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Sam2.5k
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Posts by Sam

<prev • 383 results • page 1 of 39 • next >
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Answer: C: What suggestive line at manhattan plot usually stands for?
... That line is kinda selected arbitrarily. As the genome wide significant threshold is 5e-8, a "suggestive" line of 5e-7 is usually used because it is one level up. Though in most case, the suggestive line isn't that useful and are sometime use to make the exaggerate the finding of the study ...
written 5 days ago by Sam2.5k
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Comment: C: Polygenic Risk Score analysis
... Yes, you can, but beware that using only the significant SNPs tends to generate underpowered PRS and if the study of interest use SNPs that are outside of the genome wide significance threshold, then it is likely that you won't have the information required to regenerate the score ...
written 16 days ago by Sam2.5k
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Answer: A: Linear regression on subsets of data corresponding to two factor combination
... Assuming your file is called data.txt library(data.table) dat <- fread("data.txt") results <- dat[,.(Pvalue=summary(lm(Predator.mass~Prey.mass))$coefficient[2,4], beta=summary(lm(Predator.mass~Prey.mass))$coefficient[2,3], r2=summary(lm(Predator.mass~ ...
written 27 days ago by Sam2.5k
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Comment: C: Polygenic Risk Score analysis
... You can also look into [our tutorial][1]. However, I guess what you are asking is slightly different, in that you already got PRS associated with disease and you've got a new genome that you want to calculate the Score on. For that, you'll need to know what SNPs were used for the construction and wh ...
written 4 weeks ago by Sam2.5k
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Comment: C: No Module Eigen values in grey module in WGCNA?
... Grey module is reserved as the "null module", where all genes that doesn't fall into other modules were assigned to the grey module ...
written 4 weeks ago by Sam2.5k
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Comment: C: how to use glm function to predict the factor in value
... Do you mean a model like Value ~ Cluster + Sample? If that's the case, you can just run glm in R with glm(Value~Cluster+Sample, data=data, family=binomial) Where data contains the data.frame. R should automatically dummy coded the categorical variables. ...
written 5 weeks ago by Sam2.5k
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Comment: C: Small demo bioinformatics workflows which don't require reference data?
... We have a small demonstration for polygenic risk score analysis. We simulated data using the 1000 genome and the resulting file size, after compression is around 100M. Maybe you can use that? Website is [here][1] [1]: https://choishingwan.github.io/PRS-Tutorial/ ...
written 9 weeks ago by Sam2.5k
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Comment: C: R error: vector memory exhausted
... you can in theory run the above script per small part of the file. Then you can combine the data and do a unique again in the very end ...
written 9 weeks ago by Sam2.5k
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Comment: C: R error: vector memory exhausted
... Assume your data file is called dat, will the following code work? (Replace 0.05 with threshold you want) filter <- apply(dat, 1, function(x){sum ( is.na(x))/length(x) >= 0.05; }) result <- unique(dat[!filter]) ...
written 9 weeks ago by Sam2.5k
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Answer: A: Disease risk calculation
... You can read our paper [here][1]. Here's a list of some PRS software: [PRSice][2], [lassosum][3], [LDpred][4], [PRS-CS][5] and [SBayesR][6] A tutorial can be found [here][7] [1]: https://www.biorxiv.org/content/10.1101/416545v1 [2]: http://www.prsice.info/ [3]: https://github.com/tshmak/la ...
written 10 weeks ago by Sam2.5k

Latest awards to Sam

Scholar 4 weeks ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 11 weeks ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Method for analyzing Targeted re-sequencing based on Ligation Mediated PCR?
Appreciated 9 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Student 13 months ago, asked a question with at least 3 up-votes. For Interpretation Of Differential Exon Usage Results
Great Question 14 months ago, created a question with more than 5,000 views. For Piping Markduplicates
Popular Question 21 months ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 2.5 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 2.9 years ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis
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