do_elbow_rnaseq: Calculates fold values from an MArrayLM object.

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

Description

Performs the ELBOW fold change test on an CountDataSet from DESeq object. This is a wrapper class to help integrate the ELBOW method into Bioconductor. followed tutorial from: http://cgrlucb.wikispaces.com/Spring+2012+DESeq+Tutorial

Usage

  do_elbow_rnaseq(rnaSeq)

Arguments

rnaSeq

is the CountDataSet object to analyze.

Value

a matrix specified as follows

• columns — (1) “up_limit”, the upper ELBOW fold-change cut-off value; (2) “low_limit”, the lower ELBOW fold-change cut-off value

• rows — one row per sample, specified by the parameter “columns.”

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

		# obtain the elbow limit for the dataset
		# the final step in the analysis pipeline
		do_elbow_rnaseq(results)

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