R-tutorial - Revision history

imported>Weigang at 19:25, 17 March 2019

2019-03-17T19:25:57Z

← Older revision		Revision as of 19:25, 17 March 2019
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	* Type q() to quit. Answer "y" to save workspace		* Type q() to quit. Answer "y" to save workspace
	* To reload and restore workspace, go to "C:/Users/instructor/Documents/human.genes" and double click on the file "human.gene"		* To reload and restore workspace, go to "C:/Users/instructor/Documents/human.genes" and double click on the file "human.gene"
			* [http://diverge.hunter.cuny.edu/~weigang/hg.html R Markdown]

imported>Weigang at 18:57, 2 May 2016

2016-05-02T18:57:35Z

← Older revision		Revision as of 18:57, 2 May 2016
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	* Retrieve and edit a command by pressing "up" or "down" arrows		* Retrieve and edit a command by pressing "up" or "down" arrows
	* Retrieve commands by using the search box on the "History" table		* Retrieve commands by using the search box on the "History" table
	* Type q() to quit		* Type q() to quit. Answer "y" to save workspace
			* To reload and restore workspace, go to "C:/Users/instructor/Documents/human.genes" and double click on the file "human.gene"

imported>Weigang at 18:50, 2 May 2016

2016-05-02T18:50:34Z

← Older revision		Revision as of 18:50, 2 May 2016
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	hg$Length <- hg$Gene.End - hg$Gene.Start + 1 # add a column for gene length; access variables by pressing "Tab" after "$" (auto-completion)		hg$Length <- hg$Gene.End - hg$Gene.Start + 1 # add a column for gene length; access variables by pressing "Tab" after "$" (auto-completion)
	hist(hg$Length, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long		hist(hg$Length, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long
			hist(log10(hg$Length), br = 200)
	mean(hg$Length) # not representative, super-long genes carry too much weight to the average length		mean(hg$Length) # not representative, super-long genes carry too much weight to the average length
	median(hg$Length) # More representative. Use median for a variable not normally distributed		median(hg$Length) # More representative. Use median for a variable not normally distributed
	summary(hg$Length) # Show all quartiles		summary(hg$Length) # Show all quartiles
	boxplot(Length ~ Chromosome, data = hg) show gene length by chromosomes		boxplot(log10(Length) ~ Chromosome, data = hg) show gene length by chromosomes
	write.csv(hg, "hg.csv", row.names = FALSE) # save into a file		write.csv(hg, "hg.csv", row.names = FALSE) # save into a file
	hg <- read.csv("hg.csv") # read back into R		hg <- read.csv("hg.csv") # read back into R

imported>Weigang at 13:51, 2 May 2016

2016-05-02T13:51:07Z

← Older revision		Revision as of 13:51, 2 May 2016
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	* Select "Yes" for column heading. Rename the data set if you wish (short but informative names, e.g., human.genes). Do not use spaces, use dot or underscore as name delimiters (e.g., "human.genes" or "human_genes", but never "human genes") Same rule for column or row names		* Select "Yes" for column heading. Rename the data set if you wish (short but informative names, e.g., human.genes). Do not use spaces, use dot or underscore as name delimiters (e.g., "human.genes" or "human_genes", but never "human genes") Same rule for column or row names
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	hg~~.len~~ <- hg$Gene.End - hg$Gene.Start + 1 # ~~calculate~~ gene length; access variables by pressing "Tab" (auto-completion)		dim(hg)
	hist(hg~~.len~~, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long		head(hg)
	mean(hg~~.len~~) # not representative, super-long genes carry too much weight to the average length		tail(hg)
	median(hg~~.len~~) # More representative. Use median for a variable not normally distributed		hg$Length <- hg$Gene.End - hg$Gene.Start + 1 # add a column for gene length; access variables by pressing "Tab" after "$" (auto-completion)
	summary(hg~~.len~~) # Show all quartiles		hist(hg$Length, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long
	~~log.len <- log10~~(~~hg.len); hist(log.len~~, br=~~200~~) ~~# Log of~~ gene length ~~is more normally distributed~~		mean(hg$Length) # not representative, super-long genes carry too much weight to the average length
	~~mean(log.len); median(log.len) # They should be similar, since log.len is normal~~		median(hg$Length) # More representative. Use median for a variable not normally distributed
	~~boxplot(hg$Gene.End-hg$Gene.Start+1 ~ hg$Chromosome)~~		summary(hg$Length) # Show all quartiles
			boxplot(Length ~ Chromosome, data = hg) show gene length by chromosomes
	write.csv(hg, "hg.csv", row.names = FALSE) # save into a file		write.csv(hg, "hg.csv", row.names = FALSE) # save into a file
	hg <- read.csv("hg.csv") # read back into R		hg <- read.csv("hg.csv") # read back into R
	~~boxplot(Gene.End - Gene.Start + 1 ~ Chromosome, data = hg) # show gene length by chromosomes~~
	</syntaxhighlight>		</syntaxhighlight>
	* Export a PDF or image		* Export a PDF or image

imported>Weigang at 17:14, 1 May 2016

2016-05-01T17:14:29Z

← Older revision		Revision as of 17:14, 1 May 2016
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	# Install R & RStudio on your home computer		* Install R & RStudio on your home computer
	## R from this website: https://mirrors.nics.utk.edu/cran/		** R from this website: https://mirrors.nics.utk.edu/cran/
	## R studio from this website: https://www.rstudio.com/		** R studio from this website: https://www.rstudio.com/
	# Create a new project by navigating: File \| New Project \| New Directory. Name it project file "genes"		* Create a new project by navigating: File \| New Project \| New Directory. Name it project file "genes"
	# Import abalone data set: Tools \| Import DataSet \| From Web URL, copy & paste this address: http://diverge.hunter.cuny.edu/~weigang/data-sets-for-biostat/hg.tsv2		* Import abalone data set: Tools \| Import DataSet \| From Web URL, copy & paste this address: http://diverge.hunter.cuny.edu/~weigang/data-sets-for-biostat/hg.tsv2
	# Select "Yes" for column heading. Rename the data set if you wish (short but informative names, e.g., human.genes). Do not use spaces, use dot or underscore as name delimiters (e.g., "human.genes" or "human_genes", but never "human genes") Same rule for column or row names		* Select "Yes" for column heading. Rename the data set if you wish (short but informative names, e.g., human.genes). Do not use spaces, use dot or underscore as name delimiters (e.g., "human.genes" or "human_genes", but never "human genes") Same rule for column or row names
	<syntaxhighlight lang=R">		<syntaxhighlight lang="bash">
	hg.len <- hg$Gene.End - hg$Gene.Start + 1 # calculate gene length; access variables by pressing "Tab" (auto-completion)		hg.len <- hg$Gene.End - hg$Gene.Start + 1 # calculate gene length; access variables by pressing "Tab" (auto-completion)
	hist(hg.len, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long		hist(hg.len, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long
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	median(hg.len) # More representative. Use median for a variable not normally distributed		median(hg.len) # More representative. Use median for a variable not normally distributed
	summary(hg.len) # Show all quartiles		summary(hg.len) # Show all quartiles
	~~IQR(hg.len) # 3rd Quartile - 1st Quartile, the range of majority data points, even for skewed distribution~~
	log.len <- log10(hg.len); hist(log.len, br=200) # Log of gene length is more normally distributed		log.len <- log10(hg.len); hist(log.len, br=200) # Log of gene length is more normally distributed
	mean(log.len); median(log.len) # They should be similar, since log.len is normal		mean(log.len); median(log.len) # They should be similar, since log.len is normal
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	boxplot(Gene.End - Gene.Start + 1 ~ Chromosome, data = hg) # show gene length by chromosomes		boxplot(Gene.End - Gene.Start + 1 ~ Chromosome, data = hg) # show gene length by chromosomes
	</syntaxhighlight>		</syntaxhighlight>
	# Export a PDF or image		* Export a PDF or image
	# Open a new R script, name it as "hg.R"		* Open a new R script, name it as "hg.R"
	# Select commands and save to script		* Select commands and save to script
	# Retrieve and edit a command by pressing "up" or "down" arrows		* Retrieve and edit a command by pressing "up" or "down" arrows
	# Retrieve commands by using the search box on the "History" table		* Retrieve commands by using the search box on the "History" table
			* Type q() to quit

imported>Weigang: Created page with "# Install R & RStudio on your home computer ## R from this website: https://mirrors.nics.utk.edu/cran/ ## R studio from this website: https://www.rstudio.com/ # Create a new p..."

2016-05-01T17:12:37Z

Created page with "# Install R & RStudio on your home computer ## R from this website: https://mirrors.nics.utk.edu/cran/ ## R studio from this website: https://www.rstudio.com/ # Create a new p..."

New page

# Install R & RStudio on your home computer
## R from this website: https://mirrors.nics.utk.edu/cran/
## R studio from this website: https://www.rstudio.com/
# Create a new project by navigating: File | New Project | New Directory. Name it project file "genes"
# Import abalone data set: Tools | Import DataSet | From Web URL, copy & paste this address: http://diverge.hunter.cuny.edu/~weigang/data-sets-for-biostat/hg.tsv2
# Select "Yes" for column heading. Rename the data set if you wish (short but informative names, e.g., human.genes). Do not use spaces, use dot or underscore as name delimiters (e.g., "human.genes" or "human_genes", but never "human genes") Same rule for column or row names
<syntaxhighlight lang=R">
hg.len <- hg$Gene.End - hg$Gene.Start + 1 # calculate gene length; access variables by pressing "Tab" (auto-completion)
hist(hg.len, br = 200) # plot gene-length distribution. Not normal: mostly genes are short, few very long
mean(hg.len) # not representative, super-long genes carry too much weight to the average length
median(hg.len) # More representative. Use median for a variable not normally distributed
summary(hg.len) # Show all quartiles
IQR(hg.len) # 3rd Quartile - 1st Quartile, the range of majority data points, even for skewed distribution
log.len <- log10(hg.len); hist(log.len, br=200) # Log of gene length is more normally distributed
mean(log.len); median(log.len) # They should be similar, since log.len is normal
boxplot(hg$Gene.End-hg$Gene.Start+1 ~ hg$Chromosome)
write.csv(hg, "hg.csv", row.names = FALSE) # save into a file
hg <- read.csv("hg.csv") # read back into R
boxplot(Gene.End - Gene.Start + 1 ~ Chromosome, data = hg) # show gene length by chromosomes
</syntaxhighlight>
# Export a PDF or image
# Open a new R script, name it as "hg.R"
# Select commands and save to script
# Retrieve and edit a command by pressing "up" or "down" arrows
# Retrieve commands by using the search box on the "History" table