tablesDE {maigesPack} | R Documentation |
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.
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)
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. |
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.
This function don't return any object.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
deGenes2by2Ttest
, deGenes2by2Wilcox
,
deGenes2by2BootT
, deGenesANOVA
,
maigesDE
, maigesDEcluster
.
## 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)