Man pages for PacificBiosciences/pbbamr
Interface R with PacBio BAM File Formats

chkClassHelper function for verifying arguments
combineConditionsHelper function to combine loaded data frames.
fromPhredFunction converts from Phred to error rate
getBAMNamesFromDatasetFileGet Aligned BAM Name
getFastaFileNameFromDatasetFileGet Reference Fasta File Path From Dataset
getHoleXConvert a holeNumber into the X coordinate on the chip.
getHoleYConvert a hole number into the Y coordinate on the chip.
getReadReportGet Per Read Metrics
getReferencePathGet the full path to a movie from a referenceset.xml file and...
helloHello, World!
loadAlnsFromIndexGiven a data frame returned by loadPBI and a fasta file, load...
loadDataAtOffsetsLoad BAM alignments as a list of data frames.
loadHeaderLoad BAM header
loadHMMfromBAMLoad BAM alignments as a list of list for the HMM model.
loadPBILoad PBI BAM index file
loadReadsFromIndexGiven a data frame returned by loadPBI load a list of the...
loadReferenceWindowLoad a section of the reference genome as a character string.
loadRegionsTableLoad regions table
loadSingleZmwHMMfromBAMLoad BAM alignment from a single ZMW as a list of list for...
loadSubreadsAtOffsetsLoad BAM subreads as a list of data frames.
toPhredFunction converts to Phred Scale, capping the error at a...
PacificBiosciences/pbbamr documentation built on Oct. 4, 2017, 12:07 a.m.