writeGeneResult: Write a condition-specific analysis result text file

In SpeCond: Condition specific detection from expression data

Description

writeGeneResult produces a text file containing the list of gene, if they have been detected as tissue-specific or not (S/N), for how many tissues in total, how many tissue as up-regulated, how many tissue as down-regulated, in which tissues for up-regulated and down-regulated.

Usage

writeGeneResult(L.specific.result, file.name.result.gene =
 "gene_summary_result.txt", gene.names = NULL)

Arguments

L.specific.result	the L.specific.result list of the included in the result of the main SpeCond function: generalResult$specificResult$L.specific.result
file.name.result.gene	the name of the produced file containing the list of specific genes an thier specific detection
gene.names	vector of gene's names to select a suset of genes. The default is NULL, all genes from the input matrix in SpeCond function are used

Author(s)

Florence Cavalli, [e-mail]

See Also

SpeCond,getProfile,writeSpeCondResult,writeUniqueProfileSpecificResult

Examples

library(SpeCond)
data(expressionSpeCondExample)
##Perform the condition specific detection analysis with SpeCond()
generalResult=SpeCond(expressionSpeCondExample, 
  param.detection=NULL, multitest.correction.method="BY", prefix.file="E", 
  print.hist.pv=TRUE, fit1=NULL, fit2=NULL, specificOutlierStep1=NULL)
specificResult=generalResult$specificResult

##write the result file
writeGeneResult(specificResult$L.specific.result, file.name.result.gene=
  "Example_gene_summary_result.txt", gene.names=
   rownames(expressionSpeCondExample)[1:10])

SpeCond documentation built on Nov. 8, 2020, 4:57 p.m.