User: pifferdavide

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pifferdavide100
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Italy
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3 months, 2 weeks ago
Joined:
4 years, 9 months ago
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Posts by pifferdavide

<prev • 36 results • page 1 of 4 • next >
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Comment: C: fcGENE error during conversion from .ped to .gen
... Thanks, this worked! ...
written 3 months ago by pifferdavide100
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fcGENE error during conversion from .ped to .gen
... I converted .vcf genotype file to .ped using plink like so: `./plink --vcf hgdp_wgs.20190516.full.chr22.vcf.gz --maf 0.01 --recode --out hgdp_chr22` . When I try to convert a .ped file to impute format `./fcgene --ped hgdp_22.ped --map hgdp_22.map --oformat impute --out hgdp_22_impute` I get the fo ...
fcgene format conversion imputation written 3 months ago by pifferdavide100
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Comment: A: Minor allele frequency differences between populations in 1000 Genomes
... I just randomly selected SNPs using SNPSNAP. They were not European specific. I assumed that the first population sequenced by 1000 Genomes was CEU and that there might be a bias towards European SNPs but I am not sure, just my conjecture. ...
written 2.5 years ago by pifferdavide100
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Minor allele frequency differences between populations in 1000 Genomes
... I downloaded frequencies of about 10K SNPs from 1000 Genomes. I computed the average frequency for each population ( I believe the standard reported frequency refers to the minor allele). In general, Europeans had the highest frequencies, around 40% but all the other populations had lower frequenci ...
genome snp written 2.5 years ago by pifferdavide100
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Comment: C: Converting Vcftools output to R readable format
... > fl <-  ("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz") > vcf <- readGT(fl, "hg19") Error: scanVcf: _DNAencode(): key 48 not in lookup table   path: C:\Users\Davide\Documents\genomes\chr1\ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vc ...
written 4.4 years ago by pifferdavide100
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VariantAnnotation: error from readVcf command
... I installed the package VariantAnnotation.I followed instructions to run the readVcf command: http://www.bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf I set the working directory to the folder containing the vcf file and ran the following code. I ...
R variantannotation written 4.4 years ago by pifferdavide100
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Comment: C: Converting Vcftools output to R readable format
... I installed VariantAnnotation.I followed instructions to run the readVcf command at: http://www.bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf I set the working directory to the folder containing the vcf file and ran the following code. I guess it ...
written 4.4 years ago by pifferdavide100
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Converting Vcftools output to R readable format
... I have used the following Vcftools code to calculate Fst distances from 1000 Genomes Chr 1 data. c:/path --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf --weir-fst-pop POP1.txt --weir-fst-pop POP2.txt --out fst.POP1.POP2 I need to extract the 3 variance components, name ...
vcf R vcftools snp written 4.4 years ago by pifferdavide100 • updated 4.4 years ago by Chris F.10
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Comment: C: Allele count from factor variable in R
... Brilliant! It works! ...
written 4.4 years ago by pifferdavide100
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Comment: C: Allele count from factor variable in R
... I am not sure. The process you are describing works for assigning letters to number but I do not know how to do it the other way round (assigning numbers to letters or levels of a factor). In this instance, the values are pre-assigned by R to each level according to the alphabetical order (as by def ...
written 4.4 years ago by pifferdavide100

Latest awards to pifferdavide

Popular Question 20 months ago, created a question with more than 1,000 views. For Converting Vcftools output to R readable format
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Converting Vcftools output to R readable format
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Allele count from factor variable in R
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Picking random SNPs from 1000 Genomes using Vcftools
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Converting Vcftools output to R readable format
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Allele count from factor variable in R
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Picking random SNPs from 1000 Genomes using Vcftools
Popular Question 4.4 years ago, created a question with more than 1,000 views. For R, PopGenome Package. Cannot open file
Popular Question 4.4 years ago, created a question with more than 1,000 views. For PopGenome...ReadVCF. Cannot open the file. Why?

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