quickAnalysis: quickAnalysis Function

In uebvhir/quickAnalysis: Análisis de expresión diferencial.

Description

La funci<c3><b3>n quickAnalysis realiza para una matriz de datos donde las filas corresponden a los genes y las columnas a las muestras un an<c3><a1>lisis de expresi<c3><b3>n diferencial entre dos grupos concretos. Para el an<c3><a1>lisis usa dos m<c3><a9>todos: un t.test para comparaciones multiples (tabla resultante: reT) y un an<c3><a1>lisis limma b<c3><a1>sico (tabla resultante: topTable). Adem<c3><a1>s, para aquellos genes diferencialmente expresados realiza los boxplots para cada uno de los grupos.

Usage

quickAnalysis(expres, groupingVar, min, sust, aFName = "Results",
  outputDir = ".", outputFType = NULL, pvalThreshold = 1,
  useAdjP = TRUE, plotSelected = TRUE, plot2pdf = FALSE)

Arguments

expres	a matrix-like data object containing log-expression or numeric values, with rows corresponding to genes and columns to samples.
groupingVar	factor which codes the grouping to be tested. There must be 1 or 2 groups.The length of the factor needs to correspond to the sample size.
min	minuend
sust	subtrahend
aFName	the name to the output file.
outputDir	the path to the output file.
outputFType	character string with the abbreviation for extension: "xls" or "html. Default value is NULL.
pvalThreshold	setting the threshold p-value. Default value is 1.
useAdjP	a logical value indicating use adjust p-value. Default value is TRUE.
plotSelected	A logical value indicating whether the output is a plot. Default value is TRUE.
plot2pdf	A logical value indicating whether the plot is a pdf. Default value is FALSE.

Value

genes: selected genes

resT: multtest

topTable: limma

Author(s)

Alex S<c3><a1>nchez [e-mail] , Miriam Mota [e-mail]

Examples

par(mfrow=c(2,2))
quickAnalysis(expres = exprs(sampleSet),
groupingVar = pData(sampleSet)$group,
min = "Case", sust = "Control", pvalThreshold = 0.25)

uebvhir/quickAnalysis documentation built on May 3, 2019, 2:22 p.m.