Final Report: Analysis of 1000 Genomes Data with PCA

Final project workflow for BIOSC 1540

Worked Example: PCA on SNPs data from a vcf file Part 1 - Data Preparation

Worked Example: PCA on SNPs data from a vcf file Part 2 - Data Analysis

Removing samples

description

PCA Analysis Case Study - Bird Species Morphology

Mean imputation of missing data in R

SNPs with chrom pos and genotype

n this exercise you will practice a useful step in working with high-dimensional data - removing invariant columns

SNP data are often stored in VCF files. These files organize SNPs in rows and samples (e.g. people) in columns. For analysis in R, the data, therefore, need to be converted into the correct form In this exercise, you will load a VCF file and work through the process of transposing it into the correct orientation. This will also involve converting the raw VCF data into numeric scores that can be used in PCA.

code checkpoint

vcfR package walkthrough

Portfolio: the vegan package and PCA for BIOSC 1540

Portfolio assignment for BIOSC 1540

code checkpoint for 1540 11/3/22