User: Ana

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Ana50
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Posts by Ana

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Manhattan plot in r
... still does not work .... ...
written 4 weeks ago by Ana50
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Comment: C: how to adjust a Manhattan plot for bayes factor
... OK, I got the solution after reading "Manhattan" , I changed my code to this: > manhattan(chrom1,bp= "snp_pos", chr="chrom",p="env4_p",snp = "snp", logp = FALSE, ylim=c(-20,50)) The problem was logp, If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-valu ...
written 4 weeks ago by Ana50
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how to adjust a Manhattan plot for bayes factor
... Hi all, I am trying to draw a Manhattan plot for the output of my genome-scan analysis. this is the head of my data-set (I have bayes factor for each enviornmental variable; BF_env4_p instead of p-value, ranging from -30 to +50). head(chrom1) snp_pos chrom BF_env4_p BF_env5_p ...
manhattan plot bayes factor written 4 weeks ago by Ana50 • updated 6 days ago by Biostar ♦♦ 20
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determining appropriate window size for identifying highly differentiated SNPs
... Hi al, I am trying to identify highly differentiated SNPs via window approach! I have 2 questions: first shall I try sliding window or adjacent windows? I wonder if there is any reference to help me to figure out which window size should I try? I would appreciate if you know any appropriate refere ...
window-size genome-scan written 7 weeks ago by Ana50 • updated 7 weeks ago by Kevin Blighe7.3k
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Comment: C: convert population allele count data into population allele frequency
... yesss, this is exactly what I want. thanks a lot. ...
written 7 weeks ago by Ana50
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Comment: C: convert population allele count data into population allele frequency
... Hi @Kevin Blighe, Thank you so much for your incredible help.... I think there is still a problem and I cannot use your new codes. But instead of calculating minor and major allele frequency, how can I calculate the frequency of allele 1 at each locus at odd row and allele 2 at even row to get some ...
written 7 weeks ago by Ana50
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Comment: C: convert population allele count data into population allele frequency
... Hi @Kevin Blighr. I am not quite sure about your solution. For instance if I take only the first and second row from the first column which are allele counts for alleles A and a at locus X1 in the first population then I would calculate allele frequency like this for allele A in population 1 fr ...
written 7 weeks ago by Ana50
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convert population allele count data into population allele frequency
... Hi all, I have a SNPs file contains the allele counts across populations of each SNP are represented by two lines in the file, with the counts of allele one on the first line and the counts for second allele on the second (more precisely each column corresponds to one population and the number of r ...
allele frequency alle count python written 7 weeks ago by Ana50 • updated 7 weeks ago by Kevin Blighe7.3k
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Comment: C: conditional replacing rows with 9
... Thanks so much @Pierre Lindenbaum, your code worked as well ...
written 7 weeks ago by Ana50
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Comment: C: conditional replacing rows with 9
... OK, I found a solution for that! I just wrote this little bash script that splits the snpfile, runs your python script for each file, merges them together as a single file and deletes split files in the end: #!/bin/bash ##directions ROOT_DIR=/data/sh/H/lfmm/10K_random_SNPs_good_pop ...
written 7 weeks ago by Ana50

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