User: Ana

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Ana100
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Posts by Ana

<prev • 88 results • page 1 of 9 • next >
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hypergeometric test on outlier SNPs
... Hi all, I have done some genome scan analyese with 2 different methods to identify outlier SNPs. There are some overlapping between these 2 methods. I want to know if the observed overlap between these 2 methods is any better than that obtained by chance alone? I have read different pots(https://sta ...
outliers hypergeometric test R written 8 days ago by Ana100
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TukeyHSD does not match the box plot
... Hi all, I have done anova followed by Tukey for multiple comparisons to compare the depth of coverage between different genotypes (homozygote for reference allele, homozygote for alternative allele and heterozygote) on different chromosomes. The strange thing is that, Tukey shows sifinificat differ ...
anova depth of coverage written 10 days ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes, I see you point. When to increase the dimension to 4 you will not get the error. But first, please note that the solution that Nicolas suggested computes correlation between the mean of DP for hom and het. So, it end up having 2 values and cor.test does not work for it. Second, the length of ho ...
written 10 weeks ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... No, I do not think so. I get this error from running cor.test and I run the cor.test between homozygotes.mean.common$dp (=7.61) and heterozygotes.mean.common$dp (=6.5). So only 2 values. I am not sure of this is the best approach to proceed! I am trying to find if there is any way to compute correl ...
written 10 weeks ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Not quite sure if I get your point. The error says I need to have at least 3 non-NA values for the correlation test. `cor.test(homozygotes.mean.common$dp,heterozygotes.mean.common$dp)` this computes correlation between only 2 values, which I guess is the reason of error. ...
written 10 weeks ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes, already found this. But, my data-set does not have any NA. I am not quite how this going to work. By calculating the mean I get one mean value for 0|0 genotype and one vale for heterozygote genotype. So, I will have only 2 values for the co.test! ...
written 10 weeks ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... I actually have only one potion in each data-set. Eventually I need to fix the script and run to for 1800 files. Each file only has one position. So I am guessing I do not need the second part of your code. However, when I tried `cor.test(homozygotes.mean$dp,heterozygotes.mean$dp)`, I get an error m ...
written 10 weeks ago by Ana100
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Compute correlation for depth of coverage between 2 datasets with different length in R
... Hello everyone, I am trying to compute correlation between depth of coverage for individuals with homozygote genotypes vs. individuals with heterozygote genotypes. here is the fist few lines of my datasets (note, I have only one position across all individuals): head(homozygotes) chrom ...
R correlation depth of coverage written 10 weeks ago by Ana100 • updated 10 weeks ago by zx87544.7k
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Comment: C: attaching genotypes in the vcf files to individual ID
... Yes, I get my desired output. but in all of the output files that I get from running your code I get lots of empty lines! ...
written 11 weeks ago by Ana100
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Comment: C: attaching genotypes in the vcf files to individual ID
... Yes, this works , the only problem is that I get a huge empty space after the final row. How can I get rid of this blank space? thanks for your help. ...
written 11 weeks ago by Ana100

Latest awards to Ana

Popular Question 11 weeks ago, created a question with more than 1,000 views. For how to filter vcf file based on sample DP? vcf tools does not work
Supporter 5 months ago, voted at least 25 times.

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