plot_dataset {ELBOW} | R Documentation |
A debug function for plotting data. This function plots an array or R object, and optionally draws the ELBOW limits on the plot. This function is mainly useful for the development and maintenance of the ELBOW method R package.
plot_dataset(my_data, column = NULL, upper_limit = NULL, lower_limit = NULL)
my_data |
is the object, or array, to plot. |
column |
the column in the object/array to plot, if applicable. |
upper_limit |
the upper ELBOW limit for the data (optional) |
lower_limit |
the lower ELBOW limit for the data (optional) |
# install the DESeq libraries #source("http://www.bioconductor.org/biocLite.R") #biocLite("DESeq") ## download the table library("DESeq") # the following bam file dataset was obtained from: # http://cgrlucb.wikispaces.com/file/view/yeast_sample_data.txt # it has been downloaded into this package for speed convenience. filename <- system.file("extdata", "yeast_sample_data.txt", package = "ELBOW") count_table <- read.table(filename, header=TRUE, sep="\t", row.names=1) expt_design <- data.frame(row.names = colnames(count_table), condition = c("WE","WE","M","M","M")) conditions = expt_design$condition data <- newCountDataSet(count_table, conditions) data <- estimateSizeFactors(data) data <- as(data, "CountDataSet") ## data <- estimateVarianceFunctions(data) data <- estimateDispersions(data) # this next step is essential, but it takes a long time... # so, just like a good cooking show we will skip this step # and load a finished version. #results <- nbinomTest(data, "M", "WE") # The below two code lines load a copy of the above dataset # which has already been processed by: # results <- nbinomTest(data, "M", "WE") # For your own real data, you must use: # results <- nbinomTest(data, "M", "WE")' # Instead of the two lines below: data(yeast_nbinomTest_results, package="ELBOW") results <- yeast_nbinomTest_results # plot the results w/o elbow (useful if do_elbow doesn't work) #plot_dataset(results, "log2FoldChange") # plot the results w/elbow limits <- do_elbow_rnaseq(results) plot_dataset(results, "log2FoldChange", limits$up_limit, limits$low_limit)