User: 714
714 • 90
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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
...
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... 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
714 • 90
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... Thanks so much! Sorry I forgot to mention that I am trying to perform a sliding window analysis using genomic data
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written 6.0 years ago by
714 • 90
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5 follow
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... 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 ...
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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
714 • 90
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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
714 • 90
0
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... Does anyone know a way to calculate the p-values for the corresponding r2 and D' output of LDheatmap?
Thanks
...
written 6.2 years ago by
714 • 90
• updated
6.1 years ago by
Philipp Bayer ♦ 6.6k
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... 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 ...
written 6.3 years ago by
714 • 90
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... 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.
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written 6.3 years ago by
714 • 90
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... 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
714 • 90
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