proc_chromR: Process chromR object

In vcfR: Manipulate and Visualize VCF Data

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)

Arguments

x	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

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.

Each window receives a name and its coordinates. Several attempts are made to name the windows appropriately. First, the CHROM column of vcfR@fix is queried for a name. Next, the label of the sequence is queried for a name. Next, the first cell of the annotation matrix is queried. If an appropriate name was not found in the above locations the chromR object's 'name' slot is used. Note that the 'name' slot has a default value. If this default value is not updated then all of your windows may receive the same name.

vcfR documentation built on May 29, 2024, 10:57 a.m.