User: mbk0asis

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mbk0asis200
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Korea, Republic Of
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5 years, 1 month ago
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Posts by mbk0asis

<prev • 79 results • page 1 of 8 • next >
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save plots in for loop
... Hi. I'm trying to read a list of strings and 'grep' them one by one from a data frame and draw and save the plots using R 'for loop' function. However, I got warning message and nor plots. "Warning message: In grep(cpg, colnames(dta)) : argument 'pattern' has length > 1 and only t ...
R grep for loop jpeg written 17 days ago by mbk0asis200
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coxph error : missing value where TRUE/FALSE needed
... Hi, all! I'was playing with a dummy data like below to study survival analysis. > test age status E2 E4 rs4266886 rs61822977 rs6733839 rs10202748 rs115124923 rs115675626 1 65 0 0.63 2.8 0.91 0.92 0.86 0.94 1.19 0.9 2 70 1 0.6 ...
coxph survival analysis written 6 weeks ago by mbk0asis200 • updated 6 weeks ago by Santosh Anand2.3k
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How to predict onset age using polygenic hazard score?
... Does anybody know how the authors [in this paper][1] predicted the Alzheimer onset age using Polygenic hazard score? Thanks! [1]: http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1002258 ...
alzheimer polygenic hazard score written 6 weeks ago by mbk0asis200
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Comment: C: How to calculate polygenic hazard score (PHS)?
... Thanks! I have been studying this paper but haven't figure out how to calculate that. Would you explain this in simple English or find a equation or something? It is too difficult to understand for a non-native English speaker who has no statistical background. Thank you! ...
written 8 weeks ago by mbk0asis200
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Answer: A: select DE genes
... If all of your samples have the same phenotype (cancer for example), why would you want to find DEGs? You should have at least one control sample to compare with. Or you want to see the overall expression pattern of your data? In that case, you are going to need a lot of computer power. Data wi ...
written 9 weeks ago by mbk0asis200
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Answer: A: extract DP of heterozygotes from vcf file
... try grep -Po 'DP=.*' INPUT | cut -d";" -f1 INPUT chrX 129 . G GT,GGT 27173.73 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=2.721;ClippingRankSum=-0.400;DP=2555;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.46;MQRankSum=-3.139;QD=27.54;ReadPosRankSum=-1.613;SOR=2.163 GT:AD:DP:G ...
written 9 weeks ago by mbk0asis200
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Answer: A: Download data from TCGA
... 1. Go to [GDC data portal][1] 2. Click 'Data' 3. Select types of cancer and files (RNA-seq in your case) 4. Click 'Download Manifest' and save the manifest file. 5. Install 'GDC data transfer tool (gdc-client)'. 6. Go to the directory containing the manifest file. 7. In terminal (command line) ...
written 9 weeks ago by mbk0asis200
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Comment: C: select DE genes
... DEGs between individual patients or groups (cancer vs normal)? ...
written 9 weeks ago by mbk0asis200
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Comment: C: NGS data analysis
... 'vlookup' in MS Excel might work for you. ...
written 9 weeks ago by mbk0asis200
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How to calculate polygenic hazard score (PHS)?
... Hi. A recently published paper in [PLOS medicine][1] reported that they had developed a polygenic hazard score (PHS) for quantifying individual differences in age-specific genetic risk for Alzheimer disease (AD) with hazard ratios of disease associated 33 SNPs. Later in that paper, they predicted ...
alzheimer plygenic hazard score statistics written 10 weeks ago by mbk0asis200 • updated 10 weeks ago by anp37580

Latest awards to mbk0asis

Popular Question 3 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Great Question 4 months ago, created a question with more than 5,000 views. For Finding a sequence in a fasta file
Popular Question 4 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 5 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 10 months ago, created a question with more than 1,000 views. For Pairwise2 - Biopython - weird local alignment results
Popular Question 16 months ago, created a question with more than 1,000 views. For Barcode (index) splitting
Supporter 16 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file

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