getCallsInRange: Function to get Calls In Range

In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description

Returns a list containing a character vector for each position in the range refEnd - refStart + 1.

Usage

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) 

Arguments

cmpH5	An object of class PacBioCmpH5.
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.

Value

Functions 'getCallsInRange' and 'getCallsForReads' return a lists of character vectors. Functions 'getConsensusInRange' and 'getConsensusForReads' return character vectors.

Examples

  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)

PacificBiosciences/R-pbh5 documentation built on May 7, 2019, 11:54 p.m.