Celegans {BSgenome.Celegans.UCSC.ce2} | R Documentation |
Caenorhabditis elegans (Worm) full genome as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.
This BSgenome data package was made from the following source data files:
chromFa.zip upstream1000.zip upstream2000.zip upstream5000.zip from http://hgdownload.cse.ucsc.edu/goldenPath/ce2/bigZips/See
?BSgenomeForge
and the BSgenomeForge
vignette (vignette("BSgenomeForge")
) in the BSgenome software
package for how to make a BSgenome data package.
H. Pages
BSgenome-class,
DNAString-class,
available.genomes
,
BSgenomeForge
Celegans seqlengths(Celegans) Celegans$chrI # same as Celegans[["chrI"]] if ("AGAPS" %in% masknames(Celegans)) { ## Check that the assembly gaps contain only Ns: checkOnlyNsInGaps <- function(seq) { ## Replace all masks by the inverted AGAPS mask masks(seq) <- gaps(masks(seq)["AGAPS"]) unique_letters <- uniqueLetters(seq) if (any(unique_letters != "N")) stop("assembly gaps contain more than just Ns") } ## A message will be printed each time a sequence is removed ## from the cache: options(verbose=TRUE) for (seqname in seqnames(Celegans)) { cat("Checking sequence", seqname, "... ") seq <- Celegans[[seqname]] checkOnlyNsInGaps(seq) cat("OK\n") } } ## See the GenomeSearching vignette in the BSgenome software ## package for some examples of genome-wide motif searching using ## Biostrings and the BSgenome data packages: if (interactive()) vignette("GenomeSearching", package="BSgenome")