RLEReadCounts-class {ChIPseqR} | R Documentation |
This class provides a memory efficient representation of strand specific read counts.
Objects can be created by calls of the form ReadCounts(counts, names, compress = TRUE)
or by calls
to strandPileup
.
counts
:Object of class "list"
with one component per chromosome,
containing a read counts encoded in an object of class RleList
.
Class "ReadCounts"
, directly.
signature(x = "RLEReadCounts")
: Returns length of all chromosomes represented in x
.
signature(x = "RLEReadCounts")
: Expands read counts and returns object of class ReadCounts
.
signature(x = "RLEReadCounts")
: Returns the number of reads on each chromosome, split by strand (if byStrand
is TRUE
)
signature(x = "RLEReadCounts", y = "missing")
: Generates plots of read counts.
Peter Humburg
showClass("RLEReadCounts") ## generate some very simple artificial read data set.seed(1) fwd <- sample(c(50:70, 250:270), 30, replace=TRUE) rev <- sample(c(197:217, 347:417), 30, replace=TRUE) ## create data.frame with read positions as input to strandPileup reads <- data.frame(chromosome="chr1", position=c(fwd, rev), length=25, strand=factor(rep(c("+", "-"), times=c(30, 30)))) ## create object of class ReadCounts readPile <- strandPileup(reads, chrLen=500, extend=1, plot=FALSE, compress=TRUE) names(readPile) length(readPile) sapply(readPile, sum)