Contents
PolyGeniusVariantFate
Per-variant scoring fate record
The record scores.pack.variant.fate() retains on the score matrix: a list with $ids (the
variant identities), $codes (one byte per variant per genotype: status in bits 0-2, flipped
in bit 3, strand.ambiguous in bit 4), $excluded, $counts, $n.requested, $n.flipped and
$n.strand.ambiguous. as.data.table() expands it into the full per-variant table.
Usage
S3 method for class 'PolyGeniusVariantFate'
as.data.table(x, ...)S3 method for class 'PolyGeniusVariantFate'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)S3 method for class 'PolyGeniusVariantFate'
print(x, n = 6L, ...)Arguments
| Argument | Description |
|---|---|
x | A PolyGeniusVariantFate. |
... | Unused. |
row.names | See base::as.data.frame(). |
optional | See base::as.data.frame(). |
n | Number of variants to show. |
Value
A data.table.
Invisibly returns x.
Expanded table
One row per requested variant per genotype, the schema the fate table itself carries: chr,
position, nea, ea, status, matched, flipped, strand.ambiguous, freq,
n.records, plus a leading genotype when more than one contributed.
n.records is reconstructed rather than stored: it is 0 for a variant that matched no record
and 1 for one that matched exactly once, and only a collision carries more -- which is kept
with the excluded rows. freq is NA for a scored variant; see
scores.pack.variant.fate().
See Also
Other genome-signals:
PolyGeniusGenomeSignal(),
PolyGeniusGenomeTrack