User: Sam

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Sam2.6k
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Posts by Sam

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Answer: A: Hwo to do quality control steps on UKBiobank data?
... I have a rough Nextflow pipeline for this. You can find the scripts [here][1] You can read the help message to see what file you need and you can read the script to see what actually did the script does. You will also need the GreedyRelated program I wrote to run the script, which can be found [h ...
written 1 day ago by Sam2.6k
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Comment: C: How to load 1000 genome vcf and tbi file into R
... It'd be much easier to use PLINK than to use R for this type of analysis. The error message suggested some of the SNPs has duplicated name (e.g. ".", which is typical when you convert vcf to PLINK format). You will need to do some preprocessing beforehand. Might want to look into the PLINK manual ...
written 2 days ago by Sam2.6k
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Comment: C: Effect Allele Frequency in base summary statistics for PRSs calculation
... If your goal is to filter by MAF of 0.01, then yes. ...
written 2 days ago by Sam2.6k
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Answer: A: Do you always need to clump polygenic risk scores?
... Depends on the algorithm used. If you follow the traditional p-value thresholding approach, then clumping is necessary to avoid bias by LD as suggested by you. However, if they are using more sophisticated models that already accounts for LD e.g. LDpred, lassosum, PRS-CS etc, then they don't need to ...
written 4 days ago by Sam2.6k
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Answer: A: How to load 1000 genome vcf and tbi file into R
... 1. No. They are of different format 2. if you want to work with the ped file, then you will need to convert them using PLINK. Or you can directly download the data [here][1] [1]: https://www.cog-genomics.org/plink/1.9/resources ...
written 4 days ago by Sam2.6k
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Comment: C: Genetic QC checks in R - packages and errors
... I'll usually just read in the data.frame and do the filtering manually myself. e.g. if my data.frame (`df`) has an INFO column and a MAF column and I want to filter by INFO > 0.8 and MAF > 0.05, I can do ``` res <- subset(df, INFO > 0.8 & MAF > 0.05) ``` ...
written 4 days ago by Sam2.6k
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Comment: C: Effect Allele Frequency in base summary statistics for PRSs calculation
... Opps, sorry, should be 0.99. Have now edited ...
written 4 days ago by Sam2.6k
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Comment: C: Genetic QC checks in R - packages and errors
... If that's the case, you will also need to manually install the `digest` package. (can simply use `install.packages("digest")`) ...
written 6 days ago by Sam2.6k
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Comment: C: Genetic QC checks in R - packages and errors
... Can you confirm that you've successfully install "snpReady"? snpReady seems to be dependent on "impute" which is on Bioconductor instead of CRAN and need to be installed manually with if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocMan ...
written 6 days ago by Sam2.6k
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Answer: A: Effect Allele Frequency in base summary statistics for PRSs calculation
... If you know the effective allele information, then you can simply filter the effective allele frequency as those > 0.99 and < 0.01. Because if the effective allele frequency is less than 0.01, it's the minor allele. ...
written 6 days ago by Sam2.6k

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Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Epic Question 9 weeks ago, created a question with more than 10,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Scholar 9 weeks ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 4 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 5 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For Method for analyzing Targeted re-sequencing based on Ligation Mediated PCR?
Appreciated 13 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Student 16 months ago, asked a question with at least 3 up-votes. For Interpretation Of Differential Exon Usage Results
Great Question 17 months ago, created a question with more than 5,000 views. For Piping Markduplicates
Popular Question 2.0 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 2.8 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
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Great Question 3.4 years ago, created a question with more than 5,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
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