maigesPack (version 1.36.0)

tablesDE: Save HTML or CSV tables of differentially expressed genes

Description

This function takes an object of class maigesDE or maigesDEcluster generated by functions deGenes2by2Ttest, deGenes2by2Wilcox, deGenes2by2BootT and deGenesANOVA and save HTML or CSV tables differentially expressed genes.

Usage

tablesDE(deComp=NULL, dir="./", filenames=NULL, dataID="Someone's", type=c("HTML","CSV")[1], geneID="GeneName", hsID="ClusterId", gbID="GeneId", annotID="Annot", genes=NULL, logFold=TRUE, adjP="none", sort="p.value", nDEgenes=NULL)

Arguments

deComp

object of class maigesDE.

dir

character specifying the directory to save the files.

filenames

character vector with file names to be saved, if NULL default names are given.

dataID

character giving an identifier for the dataset. If NULL the notes slot from DE.comp are used.

type

type of file to be saved. May be 'HTML' (default) or 'CSV'.

geneID

character giving the ID of label for gene symbol in the dataset.

hsID

character giving the ID of label for unigene code in the dataset.

gbID

character giving the ID of label for Genbank entry in the dataset.

annotID

character giving the ID of label for gene annotation in the dataset.

genes

character vector specifying the genes to be saved, mapped according to geneID label.

logFold

logical specifying if the fold change must be saved in log2 scale.

adjP

character string giving the type of p-value adjustment. May be 'Bonferroni', 'Holm', 'Hochberg', 'SidakSS', 'SidakSD', 'BH', 'BY' or 'none'. Defaults to 'none'.

sort

character specifying the field to be sorted, may be 'p.value' (default), 'fold' or 'statistic'.

nDEgenes

number of differentially genes to be saved in the file. Defaults to NULL to save all genes. If an integer value the function saves the nDEgenes with smaller p-values (most significantly DE genes). If a number in (0,1) nDEgenes is used as a cutoff for the p-values.

Value

This function don't return any object.

Details

We use the function mt.rawp2adjp from package multtest to adjust p-values, any information the methods implemented must be searched in their help pages. The arguments hsID, gbID and annotID are used only to improve the tables generate including links for the respective databases, but if these information are absent in the dataset they must be specified as NULL. The argument geneID must be necessarily specified, because the genes must be at least one identification.

See Also

deGenes2by2Ttest, deGenes2by2Wilcox, deGenes2by2BootT, deGenesANOVA, maigesDE, maigesDEcluster.

Examples

## Loading the dataset
data(gastro)

## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
## specifies one thousand bootstraps
gastro.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")

tablesDE(gastro.ttest) ## Save HTML tables

## To save only tables with p-value < 0.05
tablesDE(gastro.ttest, nDEgenes=0.05)

## To save only tables with 30 most significantly genes
tablesDE(gastro.ttest, nDEgenes=30)