R is an “object oriented” interactive language. I am sure all the CSCE majors reading this can give me a better definition of the term “object oriented” (and I hope you will), but in my non-CSCE way of thinking it means that data in R are organized into specific structures called “objects”, of different types, and these objects share similar qualities, or “attributes”.
# Designate samples as outlying if their Z.k value is below the thresholdthresholdZ.k = -5 # often -2.5# the color vector indicates outlyingness (red)outlierColor = ifelse(Z.k < thresholdZ.k, "red", "black")# calculate the cluster tree using flahsClust or hclustsampleTree = flashClust(as.dist(1 - A), method = "average")# Convert traits to a ...
This leaves us with a data frame with 32 rows and 15 columns. In total, there are 16 measurements from samples of ‘Het1’ and 16 measurements from samples of ‘Het2’. Because PCA requires matrix manipulations, we need the R object holding the data to be a matrix. To do this, we can get rid of the first four columns of data.
Remove objects from the current workspace. list.files List files in the current directory. ... - a set of elements organized in rows and columns, where columns can be of different types. List ... family
R code from chapter 12 of the book. Horvath S (2011) Weighted Network Analysis. Applications in Genomics and Systems Biology. Springer Book. ISBN: 978-1-4419-8818-8
Function read.table() reads the contents of a data set and creates a data frame from those contents. A data frame is essentially a matrix containing a combination of numeric variables and character strings. Use either “/” or “\\” in the path to the file. The argument “header=T” is used for a data set containing labeled columns (a ...
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