Publications by James Liu
rpub_test
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within t...
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RPUBs 11/10
This Portfolio will walk you through using PCA for what I call pseudo-cluster analysis. You will also examine the PCA scores generated by PCA, how they correlate with themselves, and how they correlate to the original data features. This will help illustrate how the vectors in a biplot relate to the original data and the layout of the points with...
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Rpubs sleep
Preliminaries Download the vegan package Only do this once, then comment out of the script. You may have already done this this for a previous assignment. ##install.packages("vegan") Load the libraries library(ggplot2) library(vegan) ## Loading required package: permute ## Loading required package: lattice ## This is vegan 2.6-4 Load the mslee...
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Software Checkpoint 11/28
This code checkpoint will make sure that you can load .vcf files on your computer. You will also review vocab and concepts related to .vcf files and SNPs. You will need to load an analyze a .vcf file on the final exam. Make notes on all of this material and include it on your notes sheet. Learning objectives This material will appear on the fina...
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DocumentSoftware Checkpoint - Setting a working directory and loading data Start Assignment
Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Main objectives By the end of this lesson you will know how to.. set a working directory in RStudio confirm the location of the working directory with getwd() confirm a file is present with and list.files(pattern = ...) load ty...
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Portfolio: Working with SNP files 1 - loading and transposing VCF files Start Assignment
NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used. Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Set a working directory and confirm a file is present with getwd() and list.files(pattern = ...) Know what it means t...
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Portfolio: Working with VCF files 2: Removing invariant columns Start Assignment
Learning objectives This lesson introduces the concept of invariant columns and why they should be removed. It also provides a function to remove them. All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Main objectives By the end of this lesson you will Understand what can lead to a column of SNP...
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In-class Exercise: Studying Natural Selection with SNPs Start Assignment
Packages Install missing package ##install.packages("kgp") Load packages library(vcfR) ## ## ***** *** vcfR *** ***** ## This is vcfR 1.13.0 ## browseVignettes('vcfR') # Documentation ## citation('vcfR') # Citation ## ***** ***** ***** ***** library(kgp) library(ggplot2) library(ggpubr) The pa...
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Portfolio: Working with VCF files 3: Removing samples with many NAs Start Assignment
Learning objectives Review the problem of missing data in SNP datasets Introduce the concept of researcher degrees of freedom Review how to locate NAs in R using is.na() and which() Outline the use of for() loops in R to carry out repetitive tasks. Review the use of regular expressions to clean text data. Introduction The data we are using to p...
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Portfolio: Working with VCF files 4: Imputation of missing data Start Assignment
Learning objectives All of this material will appear on the exam. Take notes on the workflow, functions, and concepts. Main objectives By the end of this lesson you will know how to … Identify all of the missing values in a column of a dataframe or vector Replaces all the NAs in a column with a new value, such as the mean. Know how a for() lo...
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