PolyCorr: PolyCorr

In Mass23/MetaPoly: What the Package Does (One Line, Title Case)

PolyCorr

Description

This functions computes the gene-wise correlation between the number of SNPs, and a target variable than can be either continuous, either discrete (handles two treatments). It creates a zero-inflated poisson model of the SNP count, taking the sample, log(sequencing depth), and the gene length as fixed effects. The idea is to identify genes showing signs of selective sweeps associated with the target variable. There are three inputs:

• data: the polymorphism data created by MetaPoly's "GetGenesData" function

• min_samp: the minimal number of sample having the required depth to run the correlation test.

• samp_vec: a vector that assigns each sample (vector values) to each population (vector names). The method handles two populations encoded as 0 and 1's.

Usage

PolyCorr(data, min_samp, samp_vec, p_corr = "holm")

Mass23/MetaPoly documentation built on June 14, 2022, 6:31 p.m.