Question: Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
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gravatar for rodolfobahamonde
4 weeks ago by
rodolfobahamonde0 wrote:

Link to GitHub: https://github.com/Bioconductor/GenomicFeatures/issues/15#issue-420637665

Sesion info:

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

Required packages: GenomicFeatures

Problem: In 2014 I wrote a code to obtain a genomic range object from a UCSC genome browser track and it worked fine. Nowadays, I can’t obtain the same result from the same code and function (features)

Code:

UCSCFeatureDbTableSchema(genome="hg19",
track="Txn Factor ChIP",
tablename="wgEncodeRegTfbsClusteredV3")

fdb<-makeFeatureDbFromUCSC(genome="hg19", 
track="Txn Factor ChIP",
tablename="wgEncodeRegTfbsClusteredV3")

the download process could take a lot of time

TXF_2014<-features(fdb)

TXF_2014<-sort(TXF_2014)

show(TXF_2014)
`

Output 2014:

GRanges object with 4380444 ranges and 5 metadata columns:

    seqnames   ranges strand |         bin       score    expCount                expNums      expScores
    <Rle>   <IRanges>  <Rle> | <character> <character> <character>       <character>         <character>

  ZBTB33        chr1        10074-10329      * |            585         354           2                     204,246                     354,138

   CEBPB      chr1       10150-10413      * |             585         201           1                         343                         201

   CTCF         chr1       16111-16390      * |              585         227           7                          213,612...     110,139,..

   TAF1         chr1       29199-29688      * |             585         184           1                         157                         184

   GABPA      chr1       29276-29591      * |         585         198           1                         180                         198

   ...      ...               ...    ... .         ...         ...         ...     ...          ...
   NR3C1    chr22 51221928-51222237      * |         975         325           1                          58                         325
    PHF8    chr22 51221933-51222119      * |         975         256           1                          30                         256
   CREB1    chr22 51221944-51222223      * |         975         167           1                          47                         167
     SP4    chr22 51221978-51222258      * |         975         633           1                         155                         633
    SPI1    chr22 51223762-51224058      * |         975         213           2                     107,126                     213,161
  seqinfo: 24 sequences from hg19 genome; no seqlengths

Output 2019 from the code (TXF_2014<-features(fdb)

Error in .normargSEW0(end, "end") :
'end' must be a numeric vector (or NULL)
genomicfeatures • 48 views
ADD COMMENTlink modified 4 weeks ago by Martin Morgan ♦♦ 23k • written 4 weeks ago by rodolfobahamonde0
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