getSNPCounts: Provide the number of SNPs on each gene across the...

In LZhang98/nsSNPHotspotViewer: Non-synonymous SNP Distribution Visualization

Description

Given a properly formatted dataset (see ?snpPositions), count the number of SNPs found on each gene to determine the amount of population-wide variation. This function either provides the number of unique positions on which variation occurs, or counts the total number of observations of variation across the population.

Usage

getSNPCounts(posData, removeRepeats = TRUE)

Arguments

posData	A dataset that contains 3 columns. See ?snpPositions for what this dataset must be formatted as. Each row represents a gene, and gene has 3 attributes: its id, its length, and the positions of all SNPs observed on it in the population.
removeRepeats	A boolean specifying whether observed SNPs that share the same position on the gene are to be counted more than once. Default is TRUE.

Value

A dataframe, with each row representing a gene with the following columns:

• id - The id of the gene/transcript (unchanged from input).

• length - The length of the gene/transcript (unchanged from input).

• counts - The number of (non-)unique SNPs observed.

Examples

getSNPCounts(snpPositions)
getSNPCounts(snpPositions, removeRepeats=FALSE)

LZhang98/nsSNPHotspotViewer documentation built on Dec. 31, 2020, 2:14 p.m.