Publications by Colleen Petersen
FAQ: Plot() vs. ggscatter()
What are the key differences between making a scatterplot with the regular plot() function and the ggscatter() function from ggpubr? Install the necessary packages. # install.packages("palmerpenguins") # data(penguins) library(ggpubr) ## Loading required package: ggplot2 ## Loading required package: magrittr Use the “palmerpenguins” data to...
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FAQ: Scatter Plot Point Sizing
How do we use a third variable to size points in a scatter plot? Install the necessary packages. # install.packages("palmerpenguins") # data(penguins) library(ggpubr) ## Loading required package: ggplot2 ## Loading required package: magrittr Use the “palmerpenguins” data to create a dataframe including three variables. (I needed to create t...
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Final Portfolio Assignment!
Introduction The gene and the protein it encodes which are being analyzed in this script is called GABARAP, which stands for gamma-aminobutyric acid receptor-associated protein. This protein is found in Homo Sapiens and many other species. In this script, I will be fetching information from various databases of the GABARA1 gene and associated pro...
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Question: How do I round off a vector of values in R? You might have values containing decimals stored in a vector when working in R, and want to round all of the numbers to a certain number of places. Maybe you just want to display the data rounded a certain way, or need to use and manipulate the data. You can specify this using the round() func...
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Key vocab proteinogenic amino acids regression model / line of best fit pI confidence intervals (CI) confidence ellipse correlation coefficient Selenocysteine and Pyrrolysine re-coding stop codons y = m*x + b slope intercept Key functions / packages ggpubr pander lm() coef() cor() round() Predict pI for an Selenocysteine and Pyrrolysine Amino...
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Portfolio assignment- google sheets
The goal of this exercise is to make you familiar with how to download data from Google Sheets and to briefly review some key concepts R functions and coding concepts. We’ll do the following things DOWNLOAD SPREADSHEETS SEPARATE COLUMNS OF SPREADSHEETS CREATE DATAFRAMES DOWNLOAD SEQUENCES CREATE DOT PLOTS Packages ## Google sheets download pac...
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Testing Google Sheets Access
The goal of this exercise is to make you familiar with how to download data from Google Sheets and to briefly review some key concepts R functions and coding concepts. We’ll do the following things download a list of RefSeq accessions from a Google sheet remove the NAs using na.omit() select out all but one isoform using duplicated() Packages...
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Introduction The data being plotted in these pie graphs shows the breakdown of the ancestry of all samples from genome-wide accession studies (GWAS), which was first determined in 2009 in a study by A.C. Need and D.B. Goldstein. GWAS are funded by the US National Institutes of Health (NIH), and the information, including descriptions about ancest...
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Preliminaries Load packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## clusterApply, clusterApplyLB, clusterCall, clu...
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In this exercise we’ll look at a sequence with known tandem repeats. We’ll load the data, explore it in R, then use the dotPlot() function to make various dotplots to see how changing settings for dotPlots() help make repeat patterns stand out. Add the necessary code to make this script functional. Preliminaries Load packages library(seqinr...
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