User: rbacher

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rbacher10
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Posts by rbacher

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Comment: C: How to specify transcript_ids in makeTxDbFromUCSC function in GenomicFeatures pa
... I intend to use the reduced TxDB object as input to the CHIPseeker package via: ChIPseeker::annotatePeak(peaks, tssRegion=c(-3000, 3000), assignGenomicAnnotation=TRUE, TxDb=newTxDb)​ where newTxDb only contains my genes of interest. I know the annotatePeak will let me input a GRanges object as th ...
written 19 months ago by rbacher10
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How to specify transcript_ids in makeTxDbFromUCSC function in GenomicFeatures package?
... I would like to create a TxDb object restricted to only a specific set of transcripts. However, when I set the transcript_ids, it doesn't appear to have what I assumed would be the intended effect. Instead of the TxDb object containing only with information for the given transcript, it appears to re ...
genomicfeatures maketxdbfromucsc written 19 months ago by rbacher10
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biomaRt error in getBM for hsapiens_gene_ensembl
... I'm getting the following error when I try to use the getBM() function with any attributes: > library(biomaRt) > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > getBM(c("hgnc_symbol"), "hgnc_symbol", "MLK2", mart= human)​                                                   ...
biomart written 19 months ago by rbacher10 • updated 19 months ago by romicakerketta0

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