perWindow: Investigate aligned reads in genome intervals with sliding...
In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description Usage Arguments Details Value Author(s) See Also Examples

Investigate aligned reads in genome intervals with sliding windows.

1 2	perWindow(object, chr, winsize, step, normaliseByMatches = TRUE, mem.friendly = FALSE)

`object`	object of class `AlignedGenomeIntervals`
`chr`	string; which chromosome to investigate with sliding windows
`winsize`	integer; size of the sliding window in base-pairs
`step`	integer; offset between the start positions of two sliding windows
`normaliseByMatches`	logical; should the number of reads per `AlignedGenomeInterval` be normalised by the number of genomic matches of the read sequence before summing them up in each window? (i.e. derivation a weighted sum of read counts)
`mem.friendly`	logical; argument passed on to function `interval_overlap`; if `TRUE` the less RAM and, if the `parallel` package is attached, multiple processors are used for computing the overlap, on the expense of time

The windows are constructed from the first base position onto which a read has been mapped until the end of the chromosome.

a data.frame with the following information for each sliding window on the chromosome

`chr`	string; which chromosome the interval is on
`start`	integer; start coordinate of the windows on the chromosome
`end`	integer; end coordinate of the windows on the chromosome
`n.overlap`	integer; number of read match positions inside the window. Per match position there can be one or more reads mapped, so this number always is smaller than `n.reads`
`n.reads`	numeric; number of reads which match positions inside this window; can be floating-point numbers if argument `normaliseByMatches=TRUE`
`n.unique`	integer; number of reads which each only have one match position in the genome and for which this position is contained inside this window
`max.reads`	integer; the maximal number of reads at any single one match position contained inside this window
`first`	integer; coordinate of the first read alignment found inside the window
`last`	integer; coordinate of the last read alignment found inside the window

The result is of class data.frame and in addition of the (S3) class slidingWindowSummary, which may be utilized by follow-up functions.

Joern Toedling

AlignedGenomeIntervals-class

  exDir <- system.file("extdata", package="girafe")
  exA   <- readAligned(dirPath=exDir, type="Bowtie", 
    pattern="aravinSRNA_23_no_adapter_excerpt_mm9_unmasked.bwtmap")
  exAI  <- as(exA, "AlignedGenomeIntervals")
  exPX  <- perWindow(exAI, chr="chrX", winsize=1e5, step=0.5e5)
  head(exPX[order(exPX$n.overlap, decreasing=TRUE),])