step4: step4

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

Example output of the Fluo_modeling function

Usage

data("step4")

Format

The format is: List of 39 $ index : int [1:246] 1 2 3 4 5 6 7 8 9 10 ... $ samples : chr [1:246] "1772-062-248_A01" "1772-062-248_A03" "1772-062-248_A04" "1772-062-248_A06" ... $ batch : chr [1:246, 1:2] "1772-062-248" "1772-062-248" "1772-062-248" "1772-062-248" ... $ Size : num [1:246] 31 19 152 43 59 21 72 81 31 56 ... $ corrected.exprs : num [1:246, 1:2] 34.3 11.96 31.95 19.7 9.95 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:2] "Green" "Red" $ corrected.transformed.exprs : num [1:246, 1:2] 3.54 2.48 3.46 2.98 2.3 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:2] "Green" "Red" $ correctedAreas : num [1:246] 3.43 2.94 5.02 3.76 4.08 ... $ areacut : num 49 $ transformation : chr "log" $ image.type : chr [1:3] "BF" "Green" "Red" $ dateIndex : chr "WedMar2313:29:522016" $ single.batch.analysis : num 5 $ BGmethod : chr "normexp" $ maxMix : num 3 $ prior.pi : num 0.1 $ flex.reps : num 5 $ flexmethod : chr "BIC" $ RNG : NULL $ GAPgroups : num [1:246, 1:2] 3 6 2 6 6 6 4 6 5 4 ... $ clusterFUN : chr "kmeans" $ normal.sigma : num 200 $ centroids : num [1:7, 1:3] 2 1 5 4 3 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:3] "Cluster" "Green" "Red" $ fixClusters : num 0 $ Kmax : num 15 $ B.kmeans : num 5 $ Path : num [1:6] 6 3 5 4 2 1 $ Path.type : chr [1:2] "circular" "clockwise" $ UpdatedPath : num [1:7] 1 2 3 4 5 6 7 $ DataSorts : chr [1:246, 1:2] "0.453392432450554" "0.0087217837649943" "0.201631879709111" "-0.395060882232867" ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:2] "Distance" "Pseudotime" $ DDHFupdate : logi FALSE $ corrected.VStransformed.exprs: num [1:246, 1:2] 93.7 87.7 90.3 89.3 87.7 ... $ VSmethod : chr "DDHFmv" $ Progression : num [1:246, 1:2] 77 18 201 22 31 11 169 34 119 171 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:2] "Pseudotime" "transf.Difference" $ Updated.groups : num [1:246] 2 1 5 1 1 1 4 1 3 4 ... $ CPs : num [1:6] 56 93 140 178 206 229 $ CPmethod : chr "ECP" $ CPsig : num 0.01 $ CPgroups : num 5 $ CPmingroup : num 10

Value

example intermediates

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.