Obtain HEK293 genome data

Source: R/cnv.R

Functionality for retrieving genomic data for different lineages of the human embryonic kidney HEK293 cell line. Returned genomic coordinates are based on the hg18 human genome assembly. See references.

getHEK293GenomeTrack(
  track = c("cnv.hmm", "cnv.snp"),
  cell.line = "293T",
  cache = TRUE
)

Arguments

track

character. Genome track to retrieve. Valid options include:

  • "cnvhmm": regions of copy number variation (CNV) as inferred by a hidden Markov model (HMM) algorithm,

  • "cnvsnp": CNV regions as inferred from Illumina SNP arrays

Defaults to "cnvhmm".

cell.line

character. Valid options include:

  • "293T": highly-transfective derivative of human embryonic kidney 293 cell line,

Defaults to "293T".

cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

A GRanges object storing genomic coordinates and genomic scores of regions of interest.

Examples

   cnv.hmm <- getHEK293GenomeTrack(track = "cnv.hmm", cell.line = "293T")
#> Using cached version from 2023-02-26 15:10:50