Using Biomartr To See What Is In A Region

Question

[User 1933]

I have a set of CNV regions and I want to know what genes/promoters/enhancers/etc are there. I am using Biomart under Bioconductor and in Biomart package in R, the example is like this,

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53", mart = human, attributesL  = c("chromosome_name","start_position"), martL = human)

However, I would like to do something vise verse, my input is like "chr1:100,100000" and I would like to get a list of annotation

[Neilfws]

Edited your code; I think it should read:

, attributesL  = c("chromosome_name","start_position")

Also - this code does not return "genes, promoters, enhancers etc." It returns this:

  HGNC.symbol Chromosome.Name Gene.Start..bp. Chromosome.Name.1
1        TP53              17         7565097                17
  Gene.Start..bp..1
1           7565097

Answer 1

[Neilfws]

To get genes in a region, you probably want to use getBM() and the chromosomal_region filter. For example:

getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position"), filters = "chromosomal_region", values = "17:7500000:7600000", mart = human)

  hgnc_symbol chromosome_name start_position
1                          17        7514499
2                          17        7588578
3        FXR2              17        7494548
4                          17        7517264
5        SHBG              17        7517382
6        SAT2              17        7529552
7      ATP1B2              17        7549945
8        TP53              17        7565097
9      WRAP53              17        7589389

Use:

filters <- listFilters(human)
attributes <- listAttributes(human)

to see the available filters and attributes.