Package 'Rtwobitlib'

Compiler configuration arguments for use of Rtwobitlib

Description

The pkgconfig function prints values for PKG_LIBS and PKG_CPPFLAGS variables for use in Makevars files. It is not meant for the end user. See vignette("Rtwobitlib") for more information.

Usage

pkgconfig(opt=c("PKG_LIBS", "PKG_CPPFLAGS"))

Arguments

opt	Either "PKG_LIBS" or "PKG_CPPFLAGS"

Value

The function prints the PKG_LIBS or PKG_CPPFLAGS value and returns an invisible NULL.

Examples

pkgconfig("PKG_LIBS")

pkgconfig("PKG_CPPFLAGS")

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Read/write a .2bit file

Description

Read/write a character vector representing DNA sequences from/to a file in 2bit format.

Usage

twobit_read(filepath)

twobit_write(x, filepath, use.long=FALSE, skip.dups=FALSE)

Arguments

filepath	A single string (character vector of length 1) containing a path to the file to read or write.
x	A named character vector representing DNA sequences. The names on the vector should be unique and the sequences should only contain A's, C's, G's, T's, or N's, in uppercase or lowercase.
use.long	By default the 2bit format cannot store more than 4Gb of sequence data in total. Set use.long to TRUE if your sequence data is bigger than that.
skip.dups	By default duplicate sequence names are an error. By setting skip.dups to FALSE, sequences with a duplicated name will be skipped with a warning.

Value

For twobit_read(): A named character vector containing the DNA sequences loaded from the file.

For twobit_write(): filepath returned invisibly.

References

A quick overview of the 2bit format: https://genome.ucsc.edu/FAQ/FAQformat.html#format7

See Also

twobit_seqstats and twobit_seqlengths to extract the sequence lengths and letter counts from a .2bit file.

Examples

## Read:
inpath <- system.file(package="Rtwobitlib", "extdata", "sacCer2.2bit")
dna <- twobit_read(inpath)
names(dna)
nchar(dna)

## Write:
outpath <- twobit_write(dna, tempfile())

## Sanity checks:
library(tools)
stopifnot(md5sum(inpath) == md5sum(outpath))
stopifnot(identical(nchar(dna), twobit_seqlengths(inpath)))

---

Extract sequence lengths and letter counts from a .2bit file

Description

Extract the lengths and letter counts of the DNA sequences stored in a .2bit file.

Usage

twobit_seqstats(filepath)

twobit_seqlengths(filepath)

Arguments

filepath

A single string (character vector of length 1) containing a path to a .2bit file.

Details

twobit_seqlengths(filepath) is a shortcut for twobit_seqstats(filepath)[ , "seqlengths"] that is also a much more efficient way to get the sequence lengths as it does not need to load the sequence data in memory.

Value

For twobit_seqstats(): An integer matrix with one row per sequence in the .2bit file and 6 columns. The rownames on the matrix are the sequence names and the colnames are: seqlengths, A, C, G, T, N. Columns A, C, G, T, and N contain the letter count for each sequence.

For twobit_seqlengths(): A named integer vector where the names are the sequence names and the values the corresponding lengths.

References

A quick overview of the 2bit format: https://genome.ucsc.edu/FAQ/FAQformat.html#format7

See Also

twobit_read and twobit_write to read/write a character vector representing DNA sequences from/to a file in 2bit format.

Examples

filepath <- system.file(package="Rtwobitlib", "extdata", "sacCer2.2bit")

twobit_seqstats(filepath)

twobit_seqlengths(filepath)

## Sanity checks:
sacCer2_seqstats <- twobit_seqstats(filepath)
stopifnot(
  identical(sacCer2_seqstats[ , 1], twobit_seqlengths(filepath)),
  all.equal(rowSums(sacCer2_seqstats[ , -1]), sacCer2_seqstats[ , 1])
)

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