User: Leonard Goldstein
Leonard Goldstein • 70
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Posts by Leonard Goldstein
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... exonsBy seems to be dropping a lot of genes, including MYC:
> tx <- makeTxDbFromBiomart()
> txs_by_gene <- transcriptsBy(tx, "gene")
> exs_by_gene <- exonsBy(tx, "gene")
> length(txs_by_gene)
[1] 63967
> length(exs_by_gene)
[1] 36751
> subsetByOverlaps(txs_by_gene, GRang ...
written 11 months ago by
Leonard Goldstein • 70
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... It looks like MYC is missing from the TxDb object you created, so this is a question about the makeTxDbFromBiomart function in the GenomicFeatures package. Maybe repost your question and add GenomicFeatures as one of the tags, and hopefully someone can help. Alternatively you can try using one of th ...
written 11 months ago by
Leonard Goldstein • 70
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... Hi Magda,
Can you please provide more details -- what commands were used to generate the SGFeatureCounts object and what package versions were used i.e. output of sessionInfo(). For larger analyses I strongly recommend not to use wrapper functions like analyzeFeatures() and instead run individual a ...
written 11 months ago by
Leonard Goldstein • 70
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Answer:
A: SGSeq error on getBamInfo
... The error message should list the problematic files but it returns an empty string. Looks like something went wrong that was not caught by the internal checks (probably unrelated to the XS tag). Are your BAM file paths correct and are index files present? You can try running the following and see if ...
written 12 months ago by
Leonard Goldstein • 70
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... Hi, since I can't reproduce the problem it is difficult to troubleshoot. As an alternative to TxDb objects, the convertToTxFeatures function also accepts a GRangesList of exons grouped by transcript. So you could try something like this
> tx <- exonsBy(hsaEnsembl, "tx", use.names = TRUE)
> ...
written 12 months ago by
Leonard Goldstein • 70
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... I could run this without any issues. If the problem persists maybe you can try reinstalling R and Bioconductor?
> library(GenomicFeatures)
> library(SGSeq)
> hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
> txf <- convertToTxFeatures(hsaEnsembl)
>
> se ...
written 13 months ago by
Leonard Goldstein • 70
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... Hi Sylvain,
Yes variantID() and eventID() are accessor functions for metadata columns in the SGVariant/Counts objects. You can see all available columns by typing mcols(sgv.counts). To extract gene names you can simply use geneNames(sgv.counts). Note this will return an empty CharacterList unless ...
written 13 months ago by
Leonard Goldstein • 70
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... Hi Sylvain,
Not sure I completely follow your question. You seem to be confusing SGFeatureCounts and SGVariantCounts objects. The idea behind section 11 of the vignette is to test for differential splice variant usage within a splice event, rather than differential exon usage within a gene. This a ...
written 14 months ago by
Leonard Goldstein • 70
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... Based on the error message it looks like you are working with less than 4 samples, but you try to make plots for columns 1-4 of the SGFeatureCounts object. Regarding out-of-bound plots, the vignette includes several examples on how to specify what genomic regions to include in the plots. Please have ...
written 14 months ago by
Leonard Goldstein • 70
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... The input for getBamInfo is a data.frame with columns sample_name and file_bam (see example below). Please read the vignette or help pages.
> si <- data.frame(sample_name = c("a", "b"), file_bam = c("file_a.bam", "file_b.bam"), stringsAsFactors = FALSE)
> si <- getBamInfo(si)
...
written 14 months ago by
Leonard Goldstein • 70
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