plot_dataset: plots data to see if it matches an elbow distribution.

In ELBOW: ELBOW - Evaluating foLd change By the lOgit Way

Description

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.

Usage

  plot_dataset(my_data, column = NULL, upper_limit = NULL,
    lower_limit = NULL)

Arguments

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)

Examples

# install the DESeq libraries
		#if (!requireNamespace("BiocManager", quietly=TRUE))
    		#install.packages("BiocManager")
		#BiocManager::install("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)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

ELBOW documentation built on Nov. 8, 2020, 8:14 p.m.