ENCODE eCLIP peak calls from the HepG2 (hepatocellular carcinoma) cell line, provided for testing and demonstration of RNAPeaks visualization and analysis functions.
Format
A data frame with the following columns:
- chr
Chromosome identifier (without "chr" prefix, e.g., "1", "X")
- start
Peak start coordinate
- end
Peak end coordinate
- tag
RBP name or peak identifier
- score
Peak score or confidence value
- strand
Genomic strand ("+" or "-")
Source
ENCODE Project (https://www.encodeproject.org/)
Examples
data(HepG2_bed)
head(HepG2_bed)
#> V1 V2 V3 V4 V5 V6 V7 V8
#> 1 chr12 123510272 123510372 AGGF1 RILPL1 - 10.39385 9.13816e-09
#> 2 chr19 4036075 4036174 AGGF1 PIAS4 + 10.17775 9.13816e-09
#> 3 chr19 4035875 4035975 AGGF1 PIAS4 + 9.93753 1.35672e-08
#> 4 chr13 29558255 29558355 AGGF1 SLC7A1 - 9.91781 9.70116e-09
#> 5 chr6 2376477 2376576 AGGF1 GMDS-DT + 9.80050 9.13816e-09
#> 6 chr2 10312403 10312503 AGGF1 HPCAL1 + 9.74314 1.45070e-08
if (FALSE) { # \dontrun{
data(HepG2_bed)
data(gtf_human)
PlotGene(bed = HepG2_bed, geneID = "GAPDH", gtf = gtf_human)
} # }