helpers: helper functions
In h5vc: Managing alignment tallies using a hdf5 backend

Description Usage Arguments Details Value Author(s) Examples

These functions are helpers for dealing with tally data stored in HDF5 files.

formatGenomicPosition( x, unit = "Mb", divisor = 1000000, digits = 3,
nsmall = 1 )
encodeDNAString( ds )
defineBlocks( start, stop, blocksize )
getChromSize( tallyFile, group, dataset = "Reference", posDim = 1 )

`x`	Numerical genomic position
`unit`	Which unit to convert the position to
`divisor`	divisor corresponding to the unit, i.e. 'Mb' -> `1e6`, 'Kb' -> `1e3`
`digits`	number of digits to keep
`nsmall`	nsmall parameter to the format function
`ds`	A DNAString object to be encoded in the HDF5 tally file specific encoding of nucleotides.
`start`	first position
`stop`	last position
`blocksize`	size of blocks
`tallyFile`	Tally file to work on
`group`	Group within `tallyFile` that we want to find the chromosome size for
`dataset`	Datset to extract chromosome size from - default is "Reference"
`posDim`	Which dimension of the dataset describes the genomic position

formatGenomicPosition: Helps formatting genomic positions for annotating axes in mismatch plots etc.

encodeDNAString: This translates a DNAString object into a comaptible encoding that can be written to a HDF5 based tally file in the Reference dataset. Since the Python script for generating tallies only sets the Reference dataset in positions where mismatches exists updating the Reference dataset becomes necessary if one would like to perform analysis involving sequence context (GC-bias, mutationSpectrum, etc.)

defineBlocks: This function returns a data.frame with the columns Start and End for blocks of size blocksize spanning the interval [start, stop].

getChromSize: This function is a helper to quickly look-up the chromosome size of a given group and tally file.

formatGenomicPosition: formatted genomic position, e.g. "123.4 Mb"

encodeDNAString: A numeric vector encoding the nucleotide sequence provided in ds according to the scheme c("A"=0,"C"=1,"G"=2,"T"=3).

defineBlocks: A data.frame with the columns Start and End for blocks of size blocksize spanning the interval [start, stop].

getChromSize: Returns a numeric that is the size of the chromosome.

Paul Pyl

  formatGenomicPosition(123456789)
  library(Biostrings)
  lapply( DNAStringSet( c("simple"="ACGT", "movie"="GATTACA") ), encodeDNAString )
  getChromSize( system.file("extdata", "example.tally.hfs5", package="h5vcData"), "/ExampleStudy/16" )