appends this information to the data frame. This function. cex.sub=1, lwd=4, pch=20, xlab="x label", ylab="y label", main="My # Opens general help page for regular expression support in R. # The grep function can be used for finding patterns in strings, here letter. By default, the boxplot will be vertical, but you can change the orientation setting the horizontal argument to TRUE. # Similarly, one can compute the standard deviation for large data frames by avoiding loops. Note: users should execute either step (2.1) or (2.2), but not both! # Same as before, but with 0.5 increments. # Generates the same plot as above, but on log scale. # Syntax to access columns, rows and dimensions in arrays with more than two dimensions. # Commands to perform a correlation # Plos bar histogram of the PM ('pm') or MM ('mm') log intensities of 1st array. symbols can be, with the 'pch' argument, while their size is, can be changed with the 'cex. # Retrieves GO IDs for set of Affy IDs and then the corresponding GO term for first Affy ID. The FILENAME= option allows you to specify an automatic variable to store the name of the current input file. # Creates the sample vectors 'x' and 'y'. where the different, # Example how a list of test sets For viewing PCA plots in 3D, one can use the scatterplot3d library or the made4 library. Avoid spaces in object, row and column names. An excellent introduction into the usage of SVMs in R is available in David Meyer's SVM article. # Reassignment syntax to create/replace an entire object. frame and records the corresponding p-values. # Generates sample data set of Affy ID numbers. The origin vector is only required for analyzing data from multiple This moderated t-statistics uses standard deviations. # Subsets a data frame with a query vector using the '%in%' function. The box of a boxplot starts in the first quartile (25%) and ends in the third (75%). To calculate a paired item-item distances and then assign coordinates for each item in a The color of the plotted recommended to carefully read their help documentation with, The lattice package developed by Deepayan Sarkar implements in R the Comparison operators are: == (equal), != ##############################################, #############################################################################, ###########################################################, ###############################################. A list GOHyperGAll provides similar utilities as the hyperGTest function in the GOstats package from BioConductor. If you have loaded multiple packages with similar functionality, e.g. occurances of strings across rows. Identifies all genes with at least a two fold up or down regulation and # Cuts the tree and creates color vector for clusters. You can follow the code block to add the lines and points for horizontal and vertical box and whiskers diagrams. 'infile' and '.Rout' is appended to outfile. (not). The included packages are a 'personal selection' To use the installed R and BioConductor packages in R, you have to load them first. Uses available values to perform calculation while ignoring the 'NA' # The function In addition, the Consense library contains a variety of functions for comparing cluster sets, and the mclust02 library contains an implementation of the variation of information criterion described by M. Meila (J Mult Anal 98, 873-895). # Creates 5 by 2 index array ('i') and fills it with the values 1-5, 5-1. Both of them work the same way and in both directions. X systems. If you are wondering how to make box plot in R from vector, you just need to pass the vector to the boxplot function. # Transposes 'my_array'; a more flexible transpose function is 'aperm(my_array, perm)'. # Function 'pairwise.filter' takes the output from 'pairwise.comparison' and filters for significant changes. sets: a/(a+b+c). The result is plotted as heatmap. ```{r simpleplot} plot(x) ``` Note that unlike traditional Sweave, there is no need to write `fig=TRUE`. # To remove non-matching rows, use the argument setting 'all=F'. because the author uses them often for his own teaching and research. properly preprocessed, it is especially important to carefully read the # Computes the Jaccard Index for clV1 and clV2, where values close to 0 indicate low similarities and values close to 1. diagram) is a graphical representation of a five-number summary, which reorder a dendrogram and print out its labels. # Lays out vector Principal components analysis (PCA) is a data reduction technique # Notation for returning the value of an The TRUE/FALSE arguments control the layout of the plot. # Retrieves rows with column matches specified in a query vector. # Combine RMA intensities, P/M/A calls plus their wilcoxon p-values in one data frame. # The arguments 'labRow' and 'labCol' allow to provide custom labels or to omit the printing of the labels as shown here. components or modes of the following four types: numeric, character, Identify the overlap of the significant changes between the RMA and MAS5 data. by the mean of its assigned data points. Google Docs imports and exports are described here: There are three possibilities to subset data objects: (1) Subsetting by positive or negative index/position numbers, (2) Subsetting by same length logical vectors. # Provides the assignment of rows items to the SOM clusters. stores the corresponding gene identifiers, # computations for column aggregates (here: columns 1-2 and 3-4) after # Loads "affy" and "simpleaffy" packages. # Shows how to select color schemes with the RColorBrewer library. # Calculates the # When the analysis is started from Affy Cel files, one can create the required expression matrix or data frame for input. Subsequent exports to the same file x <- c(1, 2, 3); x; is.numeric(x); first line to my_script.R file: # can be found on the help pages: '$ R CMD BATCH --help' or '> ?BATCH'. The approximately unbiased p-value (AU) is computed by multiscale bootstrap resampling. # or 'R --help'; provides help on R environment, more detailed information on page 90 of 'An Introduction to R'. returns the corresponding x-y-coordinates after clicking on right mouse # Returns logical vector of "FALSE" and "TRUE" strings. Self-organizing map (SOM), also known as Kohonen network, is a By adding a "-" sign one can reverse the sort order. function. Prints and modifies the color palette which is used when the argument # Sets the number of digits to print in numeric output to 3 digits. # Images need to be in pnm format. The e1071 package contains an interface to the C++ libsvm Perform simpleaffy QC checks: scaling factor, percent present calls, etc. Plots subcomponents specified by grouping vector after '|' in separate