windowing: Create window summaries of data

In vcfR: Manipulate and Visualize VCF Data

Create window summaries of data

Description

Create windows of non-overlapping data and summarize.

Usage

NM2winNM(x, pos, maxbp, winsize = 100L, depr = TRUE)

z.score(x)

windowize.NM(x, pos, starts, ends, summary = "mean", depr = TRUE)

Arguments

x	A NumericMatrix
pos	A vector of chromosomal positions for each row of data (variants)
maxbp	Length of chromosome
winsize	Size (in bp) for windows
depr	logical (T/F), this function has been deprecated, set to FALSE to override.
starts	integer vector of starting positions for windows
ends	integer vector of ending positions for windows
summary	string indicating type of summary (mean, median, sum)

Details

The numeric matrix where samples are in columns and variant data are in rows. The windowing process therefore occurs along columns of data. This matrix could be created with extract.gt.

The chromosome is expected to contain positions 1 though maxbp. If maxbp is not specified this can be inferred from the last element in pos.

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