Description Usage Arguments Details Value Examples
Return classifier quality values from a class/file which contains them.
1 2 3 4 5 6 7 8 | getQualityValue(h5Obj, ...)
getInsertionQV(h5Obj, ...)
getDeletionQV(h5Obj, ...)
getMergeQV(h5Obj, ...)
getSubstitutionQV(h5Obj, ...)
getDeletionTag(h5Obj, ...)
getSubstitutionTag(h5Obj, ...)
|
h5Obj |
An object of class |
... |
Extra arguments – See class documentation for |
Quality values are provided in the standard phred scaling,
QV = -10 \log_{10} p_{err}
so that a larger QV values indicates a smaller probability of the given error type.
Deletion QVs correspond to the the probability of a deletion event occuring before the indicated sequence position, and the DeletionTag value will be an uppercase ASCII-encoded DNA base (‘A’, ‘C’, ‘T’, ‘G’) or else ‘N’ if the primary pipeline did not identify a "most-likely" deleted base.
Quality values are calculated in the primary analysis pipeline based on pulse metrics.
A list of vectors of quality values.
1 2 3 4 5 6 7 8 9 | gc()
require(pbh5)
cmpH5 <- PacBioCmpH5(system.file("h5_files", "aligned_reads.cmp.h5",
package = "pbh5"))
values <- getQualityValue(cmpH5)
class(values)
length(values)
length(values[[1]])
head(values[[1]])
|
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