User: 714

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71490
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Posts by 714

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Comment: C: 1000 Genomes Ld Calculation
... Hi brentp, I tried to run your `linkage-blocks.py` script but I get the following error message: File "linkage-blocks.py", line 40 print "chrom\tstart\tend\tblock_size" ^ SyntaxError: invalid syntax ...
written 5.9 years ago by 71490 • updated 4 months ago by RamRS25k
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Comment: C: R Help: For Loop Over Range Of Number And Calculate Average Using An If Statemen
... Yes, Michael what I actually meant to say was a non-overlapping window. As I understood a sliding window can be overlapping or non-overlapping, because the term "sliding" refers to the analysis sliding across the data. ...
written 6.0 years ago by 71490
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Comment: C: R Help: For Loop Over Range Of Number And Calculate Average Using An If Statemen
... Thanks so much! Sorry I forgot to mention that I am trying to perform a sliding window analysis using genomic data ...
written 6.0 years ago by 71490
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R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
... Hi guys, I have a file (named DP.2L) which looks like this: CHROM POS SAMPLE_1 1 1168 47 1 1197 40 1 1202 45 POS ranges from 1168 to 49359284. I generated a sequence vector containin ...
R written 6.0 years ago by 71490 • updated 4.0 years ago by Biostar ♦♦ 20
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Comment: C: Fastphase To Plink Format
... I'm afraid the conversion is not that simple. The genotype for each individual is in rows. To use the example above: The output of fastPHASE (2 individuals, 11 SNP loci) ID 5906291001R01C01 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1 ID 5906291001R01C02 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 ...
written 6.0 years ago by 71490
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Comment: C: Fastphase To Plink Format
... Hi Kumar, did you ever find a solution to this? I am encountering the same problem.... ...
written 6.0 years ago by 71490
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Calculate P-Value Of Ld Using Ldheatmap Package In R
... Does anyone know a way to calculate the p-values for the corresponding r2 and D' output of LDheatmap? Thanks ...
R snp written 6.2 years ago by 71490 • updated 6.1 years ago by Philipp Bayer6.6k
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Null Allele For Snp Data Set
... Hi all, What is a null allele in the context of SNPs? As I understand it, in microsatellites a null allele occurs when the marker does not amplify via PCR. I was wondering if the same applies for SNPs? Does it simply mean a loci with missing data (i.e. ?/?; or ?/A due to low coverage, poor amplific ...
sequencing written 6.3 years ago by 71490
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Comment: C: Calculate Fis And Hwe For One Population
... Hi David, what you said makes a lot of sense, I figured that was the case...sorry to sound stupid but do you mean that I should edit the function so that across-population variance is zero?..I'm a novice in R and don't really have an idea of how to go about that. ...
written 6.3 years ago by 71490
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Comment: C: Calculate Fis And Hwe For One Population
... Hi Zev, I've tried it and as with my own data set I got "Nan" values for all three F-statistics. Do you think you could provide me with the code? ...
written 6.3 years ago by 71490

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