SpeCond (version 1.26.0)

getProfile: Create the condition-specific profile of specific matrix result from SpeCond

Description

getProfile converts a matrix of 0,1,-1 values in a matrix of one columns. Each row is transformed to a character chain of the values separated by comma.

Usage

getProfile(M.specific)

Arguments

M.specific

Is a matrix result present in the SpeCond object result: generalResult\$specificResult\$L.specific.result\$M.specific

Value

M.specific.profile

a matrix of number of row as the M.specific matrix x 2 columns. The first column "profile" is the profile: character chain of the values in M.specific separated by commas. The second column of the 2 columns: "sum.row" is the number of condition in which the genes is specific (up or down regulated)

M.specific.profile.unique

a matrix of number of unique profile * number of conditions. The columns order is the same as M.specific

M.specific.profile.table

a matrix of number of unique profile *2. The columns are: profile, nb.gene. The first column is the profile: character chain of the unique rows in M.specific separated by commas. The second column is the number of genes (rows) from M.specific which have this profile

See Also

SpeCond, writeSpeCondResult, writeUniqueProfileSpecifcResult, writeGeneResult

Examples

library(SpeCond)
data(expressionSpeCondExample)
dim(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)

##get the profiles for each gene
L.specific.result.profile=getProfile(generalResult$specificResult$L.specific.result
                                                      $M.specific)
##or
specificResult=generalResult$specificResult
L.specific.result.profile=getProfile(specificResult$L.specific.result$M.specific)