Publications by James Liu
Portfolio: PCA Analysis Case Study - Bird Species Morphology
Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Main objectives Work through a full analysis of a dataset with PCA Understand the connection between scree plots and the amount of variation explained by each PC Learn how to make a scree plot in terms of explained variation an...
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Worked Example: PCA on SNPs data from a vcf file Part 1 - Data Preparation Start Assignment
Introduction In this worked example you will replicate a PCA on a published dataset. The example is split into 2 Parts: Part 1: Data Preparation (this file) Part 2: Data analysis with PCA In this Data Preparation phase, you will do the following things: Load the SNP genotypes in .vcf format (vcfR::read.vcfR()) Extract the genotypes into an R-c...
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Worked Example: PCA on SNPs data from a vcf file Part 2 - Data Analysis Start Assignment
Introduction The example is split into 2 Parts: Part 1: Data Preparation Part 2: Data analysis with PCA (this file) Part 1 must be completed first to create a file, SNPs_cleaned.csv, that has been completely prepared for analysis. Now in Part 2, you will analyze the data with PCA. The steps here will be: Center the data (scale()) Run a PCA ana...
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James Liu Final Project Workflow
Library Loading library(vcfR) ***** *** vcfR *** ***** This is vcfR 1.13.0 browseVignettes('vcfR') # Documentation citation('vcfR') # Citation ***** ***** ***** ***** library(vegan) Loading required package: permute Loading required package: lattice This is vegan 2.6-4 library(ggplot2) library...
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James Liu Final Report
Introduction This report summarizes the analysis workflow and results of an analysis of SNPs from the 1000 Genomes Project. Data preparation Obtaining and loading data Single Nucleotide Polymorphism (SNPs) data in VCF format were obtained from the 1000 Genomes Project. Delete this when you are done. SNPs were downloaded using the Ensembl Data S...
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