lmAnalysis: Function to make the linear model analysis.

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

Function to make the linear model analysis.

Usage

lmAnalysis(exprs.filtered, design, cont.matrix,
  contrasts2test = 1:ncol(cont.matrix), anotPackage,
  Expressions_And_Top = TRUE, showParams = FALSE,
  use.dupCorr = FALSE, block = NULL, nDups = 1, comparison = "",
  outputDir = ".", ENTREZIDs = NULL, SYMBOLIDs = NULL, linksFile,
  fitFileName, csvType, rows2HTML = NULL, anotFileName)

Arguments

exprs.filtered	Dataset of filtered and normalized data.
design	Design matrix.
cont.matrix	Contrast matrix.
contrasts2test	Numeric vector that contains the number of the columns for the contrasts to analyze.
anotPackage	Annotation package.
Expressions_And_Top	If is TRUE it will do "Expresions" and the toptable.
showParams	If FALSe it won't show the lmFit parameters in the ExpressionsAndToptable.
use.dupCorr	parameter for correlated analysis to be passed to limma
block	parameter for correlated analysis to be passed to limma
nDups	parameter for correlated analysis to be passed to limma
comparison	Name of the comparations in all contrasts.
outputDir	Path of the file created.
ENTREZIDs	Name of the file for Entrez genes.
SYMBOLIDs	Name of the file for gene Symbols .
linksFile	Name of the file linksFile.
fitFileName	Name of file containing object resulting from lmAnalysis
csvType	type of csv to store the data.
rows2HTML	How many lines have to be written to HTML output
anotFileName	Name where annotations have to be saved.

Examples

## Not run: 
load("./ResultsDir/exprs.filtered.Rda")
contrasts2test <- 1:ncol(cont.matrix)
anotPackage = NULL
comparison =  "Estudi"
outputDir = "./ResultsDir"
ENTREZIDs = "entrezTable"
SYMBOLIDs = "symbolsTable"
linksFile = "Links.txt"
fitFileName = "fit.Rda"
csvType= "csv"
rows2HTML= NULL
anotFileName <- "Annotations"
runMulticore = 0
toTIFF= FALSE
fitMain <- BasicP::lmAnalysis(exprs.filtered = exprs.filtered, design = design,
cont.matrix = cont.matrix, contrasts2test = contrasts2test, anotPackage = anotPackage,
outputDir = outputDir, comparison = comparison, Expressions_And_Top = TRUE ,
showParams = FALSE , use.dupCorr = FALSE, block = NULL, nDups = 1 , ENTREZIDs = ENTREZIDs,
SYMBOLIDs = SYMBOLIDs, linksFile = linksFile,fitFileName = fitFileName , csvType=csvType,
rows2HTML = NULL, anotFileName = anotFileName)

## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.