SigGenesSAM: Identify significant genes through SAM

In TomNash/NASHMAP: Microarray Analysis Pipeline

Description

Implement SAM and compute significant genes given delta. Output will consist of all significant genes ordered by increasing q-value and decreasing d-score.

Usage

SigGenesSAM(background.subtraction.obj, class.compare.cols, 
class.compare.name, fdr.cutoff=0.1, response)

Arguments

background.subtraction.obj	Object returned from call to BackgroundSubtraction
class.compare.cols	Vector of column indices indicating which subset of arrays are to be compared for this comparison
class.compare.name	String title given to the name of the comparison
fdr.cutoff	Max FDR for SAM, will use delta value which results in max FDR below this cutoff
response	For two class unpaired: vector of 1, 2 values that indicate group membership. For two class paired: vector of -1, 1, -2, 2, etc. values that indicate pairings.

Value

A list with components

siggenes.table	Combined data frame of genes having significant positive and negative correlation
data.col	Vector of column indices containing array data
ntext	Number of leading text columns
response	Vector of array group membership, 1=control, 2=experimental
pipeline.name	Name of pipeline generated from input file name sans extension
data	Data frame of chosen normalization method data
class.compare.cols	Value entered through class.compare.cols parameter
class.compare.name	Value entered through class.compare.name parameter
symbol.index	Column index that contains gene symbol

TomNash/NASHMAP documentation built on May 9, 2019, 4:54 p.m.