Question

how to extract specific gene coordinates by passing a list of genes using homo.sapiens library

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Tharun • 0

@92c31cb5

Last seen 13 months ago

India

can we extract specific rows of data from Homo.sapiens library like
transcripts(Homo.sapiens, columns=c( "SYMBOL"=="BRCA2","ENTREZID")) or by passing specific list of gene.

missRows • 510 views

ADD COMMENT • link updated 13 months ago by James W. MacDonald 67k • written 13 months ago by Tharun • 0

score 0 · Answer 1 · 2023-10-04

> subset(transcripts(Homo.sapiens, columns = "SYMBOL"), SYMBOL == "BRCA2")
'select()' returned 1:1 mapping
between keys and columns
GRanges object with 4 ranges and 1 metadata column:
      seqnames            ranges
         <Rle>         <IRanges>
  [1]    chr13 32889617-32907524
  [2]    chr13 32889617-32973809
  [3]    chr13 32928998-32936830
  [4]    chr13 32945093-32953652
      strand |          SYMBOL
       <Rle> | <CharacterList>
  [1]      + |           BRCA2
  [2]      + |           BRCA2
  [3]      + |           BRCA2
  [4]      + |           BRCA2
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome