Process chromR objects: Process chromR object

Description

Functions which process chromR objects

Create representation of a sequence. Begining and end points are determined for stretches of nucleotides. Stretches are determined by querying each nucleotides in a sequence to determine if it is represented in the database of characters (chars).

Usage

proc.chromR(x, win.size = 1000, verbose = TRUE)
regex.win(x, max.win = 1000, regex = "[acgtwsmkrybdhv]")
seq2rects(x, chars = "acgtwsmkrybdhv", lower = TRUE)
var.win(x, win.size = 1000)
gt2popsum(x)
gt.to.popsum(x)

Arguments

object of class chromR

win.size

integer indicating size for windowing processes

verbose

logical indicating whether verbose output should be reported

max.win

maximum window size

regex

a regular expression to indicate nucleotides to be searched for

chars

a vector of characters to be used as a database for inclusion in rectangles

lower

converts the sequence and database to lower case, making the search case insensitive

...

arguments to be passed to methods

Details

The function proc_chromR() calls helper functions to process the data present in a chromR object into summaries statistics.

The function regex.win() is used to generate coordinates to define rectangles to represent regions of the chromosome containing called nucleotides (acgtwsmkrybdhv). It is then called a second time to generate coordinates to define rectangles to represent regions called as uncalled nucleotides (n, but not gaps).

The function gt2popsum is called to create summaries of the variant data.

The function var.win is called to create windowized summaries of the chromR object.