This method scores genes according with their highest expression in a set of pure samples.
markerScoreMaxcol(object)
matrix
, an object of class
ExpressionSet
, or a
MarkerList-class
object.Genes are assigned to their respective maximum expressing
column/value and returned as a MarkerList
object.
# random data matrix with rownames (needed)
x <- rmatrix(20, 3)
rownames(x) <- paste("g", 1:nrow(x), sep='_')
# compute score
markerScoreMaxcol(x)
## <object of class: MarkerList>
## Types: 1, 2, 3 (total: 3)
## Mode: numeric
## setName: NA
## geneIds: g_1, g_2, ..., g_19 (total: 20)
## geneIdType: Null
## collectionType: Null
## geneValues: 0.859171442454681, 0.832773762056604, ..., 0.681461257860065
## details: use 'details(object)'
# same thing with auto-ordering through the main interface function
extractMarkers(x, method='maxcol')
## <object of class: MarkerList>
## Types: 1, 2, 3 (total: 3)
## Mode: numeric
## setName: NA
## geneIds: g_20, g_8, ..., g_19 (total: 20)
## geneIdType: Null
## collectionType: Null
## geneValues: 0.954023226397112, 0.885700310114771, ..., 0.681461257860065
## details: use 'details(object)'
extractMarkers
,
markerScoreAbbas
,
markerScoreHSD
,
markerScoreMethod
,
markerScoreScorem
,
scoreMarkers
,
selectMarkers.markerScore_HSD
,
selectMarkers.markerScore_scorem