User: dhibar

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dhibar40
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Posts by dhibar

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JunctionSeq: using continuous covariates, is it possible?
... I'm wondering if anyone has any experience using continuous covariates in a JunctionSeq model for testing differential exon usage (DEU)? From the readJunctionSeqCounts function description it says: "design A data frame containing the condition variable and all desired covariates. All variables sho ...
junctionseq R sva written 3.0 years ago by dhibar40 • updated 3.0 years ago by Charles Warden7.3k
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Comment: C: adding SNP proxies to a plink dataset
... That sounds reasonable to me. I don't see why --merge would cause a problem here. One thing to keep track of though is if you have a pruned data set that you remove the SNPs selected in the pruning procedure that are in LD with the SNPs your are merging in. ...
written 3.5 years ago by dhibar40
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Comment: C: High number of significant DE genes with low baseMean, is this abnormal?
... Yes, that's an even simpler version of it. The DESeq() function is a wrapper for the SizeFactors, Dispersions, and WaldTest. ...
written 3.6 years ago by dhibar40
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Comment: C: merlin .ped file
... You can provide a "linking file" that lists the full set of subjects like mentioned above with the Ped file that has your genotypes. In merlin you would do this by separating them with a comma: merlin -p familystructure.ped,pheno.ped -d familystructure.dat,pheno.dat  [...] ...
written 3.8 years ago by dhibar40
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Answer: A: merlin .ped file
... You have to include an entry for each parent in the Ped file even if they are missing. Also, even if a parent is missing you should give them a non-zero ID if the other parent isn't missing. So if the parent (father) is missing from family 1 it currently looks like this: Family1 Sib1 Father0 Mother ...
written 3.8 years ago by dhibar40
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Comment: C: Plot with locuszoom and chr:pos SNPs
... Can you give a screenshot or more details about the other the options you are selecting in LocusZoom? Is it possible the region and flanking region you specified doesn't include any SNPs from your results list? Or maybe they aren't being read in properly because the default delimiter is "Tab" and yo ...
written 3.8 years ago by dhibar40
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RNAseq Analysis of Samples from Multiple Ancestries
... I am wondering if it is possible or if there is a common practice for differential gene expression comparisons when the samples come from different ethnic/ancestral backgrounds? In GWAS it is common to test for association within a single ancestral group to avoid population stratification, but is t ...
rna-seq written 3.9 years ago by dhibar40 • updated 3.9 years ago by Dan Gaston7.1k

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Scholar 3.8 years ago, created an answer that has been accepted. For A: merlin .ped file

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