A tbl containing the coverage from every human sample in RLBase around
"gold-standard" R-loop sites.
gs_signal(quiet = FALSE)
| quiet | If TRUE, messages are suppressed. Default: FALSE. |
|---|
A tbl object. See details.
Gold-standard R-loop sites are those which were profiled with ultra-long-read R-loop sequencing (SMRF-Seq) as described in Malig et al., 2021.. A bed file containing these sites was derived and lifted to hg38. Sites were then extended by 100kb bi-directionally and then binned into 1kb bins.
For each sample in RLBase, coverage tracks were calculated from alignments
using RLPipes. Then, coverage
tracks were summed within each of the 1kb bins using deepTools and wrangled
into a tbl.
The processing steps are described in the RLBase-data README.md.
These data are used by RLSeq::corrAnalyze() to determine how well a query sample
correlates with the samples in RLBase.
Sample of data:
| location | ERX2277510 | ERX2277511 | ERX3974959 | ... |
| chr1_67636071_67637071 | 23 | 22 | 93 | ... |
| chr1_67637071_67638071 | 44 | 39 | 84 | ... |
| chr1_67638071_67639071 | 26 | 30 | 100 | ... |
| ... | ... | ... | ... | ... |
Column desc:
location - 1kb bins within "gold-standard" R-loop regions profiled with ultra-long-read R-loop sequencing (SMRF-Seq).
ERX.../SRX... - Columns corresponding to RLBase samples (see rlbase_samples). For each sample, the total coverage (bigWig file) within the range is shown.
gss <- gs_signal()