User: Lna

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Lna0
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Posts by Lna

<prev • 30 results • page 2 of 3 • next >
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Both. The "0"s are simply spread all over the file. ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Some of the erroneous SNPs are monomorphic, some are not. The example I posted above is obviously not, but there is one SNP, for example, which is monomorphic and for which six of 28 genotypes are missing in the ped-file. ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... I ran plinkCheck to compare the files. This is the output, it implies everything should be ok: Checking SNPs against map file... OK Checking sample data and genotypes in each line of ped file... OK Checking that all samples were found in ped file... OK Then I used SNPRelate::snpgdsGDS2BED to gene ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Now I found another problem, which causes the differences between the missing rate in Plink and GWASTools. I generated the input ped file for Plink with Bioconductor: plinkWrite(genoData, pedFile="Plink", individual.col="scanID",            phenotype.col="cd34", rs.col="rsID", mapdist.col=NULL) Fo ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Concerning the association results, I am sure that the used samples are the same and even if the number of SNPs would be different (due to different filters maybe), this shouldn't make a difference for the result of a specific SNP, since association tests are independent for each SNP, are they? I'd ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... In the meanwhile, I managed to track down one of the problems that leads to a difference between the missingness filter in Plink and GWASTools. There is quite a number of SNPs on the X-chromosome in my data set, which have theta values for males that are close to 0.5 except of 1.0, which implies het ...
written 2.8 years ago by Lna0
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Thank you for your suggestions! I managed to read all my data and do all steps in the GWASTools vignette. When I started to work with plink, I compared the outcome of the two tools. I checked the number of SNPs which were included with my MAF and missing rate filter and I compared the p-values I obt ...
written 2.8 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... Ok, but does that explain why distance() gives different results depending on whether a single geneid is submitted or the geneid is part of a list of geneids? If it does not work for the genes you mentioned, shouldn't it work at all for these genes? ...
written 2.8 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... So you get NAs? Didn't you say you don't get them? Ok... let's make a simple test including the second and third option I described (Call distance() for all geneids close to my variant at once AND call distance() for each of the geneids independently): gr <- GRanges("chr1", IRanges(c(1064801), ...
written 2.8 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... Sorry, but I don't really get it... When I obtain all distances at once (like you proposed) OR when I make a loop over my variants (so I obtain a list of distances for one variant) OR when I make a loop over my variants and a nested loop over each geneid of one variant, shouldn't this give the same ...
written 2.8 years ago by Lna0

Latest awards to Lna

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Use of org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R

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