getCallsInRange: Function to get Calls In Range

Description Usage Arguments Value Examples

Description

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

Usage

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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

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  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.