getG: Calculates the G statistic

In bmansfeld/QTLseqR: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Description

The function is used by runGprimeAnalysis to calculate the G statisic G is defined by the equation:

G = 2 * ∑ n_i * ln(obs(n_i)/exp(n_i))

Where for each SNP, n_i from i = 1 to 4 corresponds to the reference and alternate allele depths for each bulk, as described in the following table:

Allele	High Bulk	Low Bulk
Reference	n_1	n_2
Alternate	n_3	n_4

...and obs(n_i) are the observed allele depths as described in the data frame. Method 1 calculates the G statistic using expected values assuming read depth is equal for all alleles in both bulks:

exp(n_1) = ((n_1 + n_2)*(n_1 + n_3))/(n_1 + n_2 + n_3 + n_4)

exp(n_2) = ((n_2 + n_1)*(n_2 + n_4))/(n_1 + n_2 + n_3 + n_4)

etc...

Usage

getG(LowRef, HighRef, LowAlt, HighAlt)

Arguments

LowRef	A vector of the reference allele depth in the low bulk
HighRef	A vector of the reference allele depth in the high bulk
LowAlt	A vector of the alternate allele depth in the low bulk
HighAlt	A vector of the alternate allele depth in the high bulk

Value

A vector of G statistic values with the same length as

See Also

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing tricubeStat for G prime calculation

bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.