getHEK293GenomeTrack: Obtain HEK293 genome data

In ccb-hms/BioPlex: R-side access to BioPlex protein-protein interaction data

Obtain HEK293 genome data

Description

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.

Usage

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.

References

http://hek293genome.org

Examples

   cnv.hmm <- getHEK293GenomeTrack(track = "cnv.hmm", cell.line = "293T")

ccb-hms/BioPlex documentation built on Aug. 5, 2023, 9:15 p.m.