User: dp0b

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dp0b20
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Posts by dp0b

<prev • 15 results • page 1 of 2 • next >
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Gemma weights widv
... Hi, I am enquiring about gemmas -widv option. I was hoping to use it to weight bulls for a gwas analysis. I was just wondering has anyone used this option and what did they base their weights on? Reliability, effective record contribution etc? I understand that a high weight represents high resid ...
gemma cattle gwas written 5 days ago by dp0b20
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Comment: C: Gwas non normally distributed-continous or categorical trait
... Thanks for you help,Ill have a look but preference is a mixed model that fits the grm ...
written 10 weeks ago by dp0b20
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Comment: C: Gwas non normally distributed-continous or categorical trait
... Thanks for getting back to me. I have edited the question and shown the distribution as you suggested. I was hoping to do the gwas using gcta but can use SAS to transform the data. ...
written 10 weeks ago by dp0b20
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Gwas non normally distributed-continous or categorical trait
... Hi, I have a trait that was measured using a assay but a large proportion of the samples where below the threshold for detection of the assay so my phenotype isnt normally distributed and transformation (log, sqrt, box-cox) isn't successful. Is it better then to treat the data as continous for gwas ...
gwas categorical continous distribution written 10 weeks ago by dp0b20
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Convert VCF dosage file into dosage only file
... Hi, Is it possibly to only output dosages from a generated vcf dosage file from minimac? Input format is ##fileformat=VCFv4.1 ##filedate=2017.7.5 ##source=Minimac3 ##contig= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL ...
vcf dosage minimac written 5 months ago by dp0b20 • updated 5 months ago by trausch830
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Gemma linear mixed model analysis with second grm format
... Hi I have been trying to run a univariate linear mixed model using GEMMA. However I was hoping to use a grm I have made else where- it is the second in grm format. The first few lines are as as follows 1 1 8.923316e-01 1 2 -5.544370e-02 1 3 1.903249e ...
software error gemma gsl gwas written 5 months ago by dp0b20
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Estimate recombination rate from linkage map
... Hi Simple question but just want to clarify how to estimate recombination rate from a genetic linkage map for a region. Recombination rate is cM/Mb so for a linkage map like below, so recombination for each snp is cM-previous cM/((position-prev position)/1000000) If I wish to estimate recombinat ...
linkage map physical map recombination written 9 months ago by dp0b20
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Eagle phasing and minimac imputation
... Hi, I wish to use eagle phasing and minimac imputation to impute to whole genome sequence. I have successfully phased my genotypes using eagle but Im struggling to read them into minimac. Minimac will tell me there are no marker overlaps between the target and reference, when there definitely is. ...
eagle minimac imputation genotypes phasing written 10 months ago by dp0b20
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scatterplotmatrix subscript labels
... Hi, I am using the car package in R to complete a scatterplot matrix with linear regression lines. I wish the column names on diagonal to be in subscript for some of the characters, is there a way I can incorporate expression into var labels? scatterplotMatrix(inbred[1:4],smooth = FALSE,ylim=c ...
R car scatterplot written 12 months ago by dp0b20 • updated 12 months ago by WouterDeCoster25k
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Fastphase cluster determination
... Hi, I want to determine the number of haplotype clusters there are in my dataset using fastphase. The results are meant to produce a _kselect file, but this never happens and fastphase always uses a K15 for the model. This is what I have been running- I wanted to test the number of clusters from 5 ...
cluster genotypes fastphase written 15 months ago by dp0b20 • updated 4 months ago by Gennady Khvorykh50

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Popular Question 9 months ago, created a question with more than 1,000 views. For Calculate LogR ratio and BAF from X and Y intensities

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