tablesDE: Save HTML or CSV tables of differentially expressed genes

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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.

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.

Value

This function don't return any object.

Author(s)

Gustavo H. Esteves <[e-mail]>

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)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.