Description Usage Arguments Value Examples
Returns a list containing a character vector for each position in the range refEnd - refStart + 1.
1 2 3 4 5 6 7 8 9 10 | getCallsInRange(cmpH5, refSeq, refStart = 1, refEnd =
getRefLength(cmpH5, refSeq), idx = 1:nrow(cmpH5))
getConsensusInRange(cmpH5, refSeq, refStart = 1, refEnd = getRefLength(cmpH5,
refSeq), idx = 1:nrow(cmpH5), blockSize = NA)
getCallsForReads(rawAlns, refStart, refEnd, strands, starts, ends)
getConsensusForReads(rawAlns, refStart, refEnd, strands, starts, ends,
fast = TRUE)
|
cmpH5 |
An object of class |
refSeq |
the reference sequence to retrieve. |
refStart |
The reference start point. |
refEnd |
The reference end point. |
idx |
The indices of the alignments to retrieve. |
rawAlns |
The raw alignments to retrive with function 'getAlignmentsRaw.' |
strands |
The low-level strand vector corresponding to the rawAlns |
starts |
The low-level starts vector corresponding to the rawAlns |
ends |
The low-level ends vector corresponding to the rawAlns |
fast |
There is a miniscule difference between the algorithm implementation. |
blockSize |
This allows someone to chunk the computation. |
Functions 'getCallsInRange' and 'getCallsForReads' return a lists of character vectors. Functions 'getConsensusInRange' and 'getConsensusForReads' return character vectors.
1 2 3 4 5 6 7 8 9 10 11 12 13 | require(pbh5)
cmpH5 <- PacBioCmpH5(system.file("h5_files", "aligned_reads.cmp.h5",
package = "pbh5"))
callsInRange <- getCallsInRange(cmpH5, 1)
head(callsInRange)
cnsInRange <-getConsensusInRange(cmpH5, 1)
head(cnsInRange)
callsForReads <-getCallsForReads(getAlignmentsRaw(cmpH5, 1), 1, 2000, 1, 1, 2)
head(callsForReads)
cc <- computeConsensus(callsInRange)
head(cc)
cfr <- getConsensusForReads(getAlignmentsRaw(cmpH5, 1), 1, 2000, 1, 1, 2)
head(cfr)
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