getProfile {SpeCond} | R Documentation |
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.
getProfile(M.specific)
M.specific |
Is a matrix result present in the SpeCond object result: generalResult\$specificResult\$L.specific.result\$M.specific |
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 |
Florence Cavalli, florence@ebi.ac.uk
SpeCond
, writeSpeCondResult
, writeUniqueProfileSpecifcResult
,
writeGeneResult
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)