User: GabrielMontenegro

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Posts by GabrielMontenegro

<prev • 152 results • page 1 of 16 • next >
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Comment: C: Placing random non-overlaping segments across genome [GenomicRanges]
... Thank you, I will check this package. Yes, the first functions looks very close to what I want to do! ...
written 3 months ago by GabrielMontenegro560
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Comment: C: Generate random genomic positions with R
... Is there a way to make random genomic ranges, but avoiding overlap between the segments? I want to randomly place non-overlapping segments (with a given length[width]) across the genome. Thanks. ...
written 3 months ago by GabrielMontenegro560
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Placing random non-overlaping segments across genome [GenomicRanges]
... I am trying to make a script that will place non-overlapping genomic ranges across the genome. Say for example I have a genomic ranges object like this: GRanges object with 301 ranges and 0 metadata columns: seqnames ranges strand [ ...
R genomicranges written 3 months ago by GabrielMontenegro560
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Rounding error in allele frequency estimates in PLINK
... I was checking allele frequencies for a dataset using `plink`. In one dataset I was using the default behavior and thus plink was outputting minor allele frequencies. In the second case, I fixed the A1 allele to a given allele. I found that in some cases, going back to MAF when fixing a given alle ...
plink snp written 5 months ago by GabrielMontenegro560
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Comment: C: Get the longest transcript in GenomicRanges
... I just found out that I can `reduce` the transcripts... which is not exactly what I want, as I think this is collapsing all the transcripts... i.e. `p.txdb <- autoplot(Homo.sapiens, which = range, stat = "reduce")` ...
written 5 months ago by GabrielMontenegro560
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Comment: C: Get the longest transcript in GenomicRanges
... Great, thanks! So, then, within the `autoplot` function, how do I select only those transcripts? I am trying to do that, but it keeps printing all transcripts. ...
written 5 months ago by GabrielMontenegro560
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Comment: C: Get the longest transcript in GenomicRanges
... I checked that, and a `TxDb` object does not contain gene names... I would like to show the name of the genes not the transcripts names. ...
written 5 months ago by GabrielMontenegro560
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Comment: C: Get the longest transcript in GenomicRanges
... Thanks for the help. I've checked which data can be retrieved from the `Homo.sapiens` object using `columns(Homo.sapiens)`, and there is actually information on the transcript start and transcript end. I think I will need to get the width first, and then modify the `Homo.sapiens` object somehow? ...
written 5 months ago by GabrielMontenegro560
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Get the longest transcript in GenomicRanges
... I am trying to plot an specific region using `ggbio`. I am using the below code that produces my desire output, except that it contains several transcript. Is it possible to only plot the longest transcript for each gene? I've not been able to access the genomic ranges object within `Homo.sapiens` t ...
R ggbio genomicranges written 6 months ago by GabrielMontenegro560
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... I just noticed that after using `--ref-allele force` some of the genotypes that were UNPHASED appear as PHASED in the new vcf file. Is there any way to avoid this from happening? ...
written 16 months ago by GabrielMontenegro560

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Popular Question 5 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
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Popular Question 14 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: how to get a subset of vcf file for specific SNPs
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Appreciated 20 months ago, created a post with more than 5 votes. For A: Interpreting Ldhat Outputs
Popular Question 20 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Popular Question 20 months ago, created a question with more than 1,000 views. For Gene plot similar to LocusZoom
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Popular Question 23 months ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Armitage's trend test for the 2x3 genotype table
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Gene plot similar to LocusZoom
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Subsetting individuals from IMPUTE2 ref files: .hap and .legend
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Getting the function of genes based on gene names

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