gene counts in Seurat after RunCCA() and AlignSubspace()
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Entering edit mode
Bogdan ▴ 620
@bogdan-2367
Last seen 6 days ago
Palo Alto, CA, USA

Dear all,

happy and healthy new year ! I would appreciate your help on scRNA-seq analysis, as I am doing a comparison between 2 scRNA-seq datasets ; I am using SEURAT package and after I use RunCCA() and AlignSubspace(), as described here :

https://satijalab.org/seurat/immune_alignment.html

please would you let me know how I can access the matrices with the appropriate (processed) gene counts (in the object below),

in order to make customized boxplots BETWEEN specific GENES that belong to distinct CLUSTERS in CONTROL vs TREATMENT1

(and TREATMENT2) ? thank you very much !

 

> str(both.combined)

Formal class 'seurat' [package "Seurat"] with 20 slots

  ..@ raw.data    :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots

  .. .. ..@ i       : int [1:10354214] 2 22 24 41 43 45 65 67 79 90 ...

  .. .. ..@ p       : int [1:3172] 0 1386 5184 7061 11913 13631 15513 17776 19993 21875 ...

  .. .. ..@ Dim     : int [1:2] 15213 3171

  .. .. ..@ Dimnames:List of 2

  .. .. .. ..$ : chr [1:15213] "Xkr4" "Rp1" "Mrpl15" "Lypla1" ...

  .. .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  .. .. ..@ x       : num [1:10354214] 3 2 2 15 1 3 1 2 1 1 ...

  .. .. ..@ factors : list()

  ..@ data        :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots

  .. .. ..@ i       : int [1:10354214] 2 22 24 41 43 45 65 67 79 90 ...

  .. .. ..@ p       : int [1:3172] 0 1386 5184 7061 11913 13631 15513 17776 19993 21875 ...

  .. .. ..@ Dim     : int [1:2] 15213 3171

  .. .. ..@ Dimnames:List of 2

  .. .. .. ..$ : chr [1:15213] "Xkr4" "Rp1" "Mrpl15" "Lypla1" ...

  .. .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  .. .. ..@ x       : num [1:10354214] 1.756 1.433 1.433 3.216 0.954 ...

  .. .. ..@ factors : list()

  ..@ scale.data  : num [1:15213, 1:3171] -0.0612 -0.0979 2.8866 -0.6214 -1.0193 ...

  .. ..- attr(*, "dimnames")=List of 2

  .. .. ..$ : chr [1:15213] "Xkr4" "Rp1" "Mrpl15" "Lypla1" ...

  .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  ..@ var.genes   : chr [1:1157] "Sprr1a" "S100a6" "Spp1" "Cartpt" ...

  ..@ is.expr     : num 0

  ..@ ident       : Factor w/ 18 levels "c1_CTRL","c1_G11",..: 5 9 15 1 5 7 1 1 7 11 ...

  .. ..- attr(*, "names")= chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  ..@ meta.data   :'data.frame': 3171 obs. of  7 variables:

  .. ..$ nGene        : int [1:3171] 1387 3799 1879 4856 1718 1884 2263 2218 1882 5230 ...

  .. ..$ nUMI         : num [1:3171] 6267 19298 5172 18883 11472 ...

  .. ..$ orig.ident   : Factor w/ 1 level "comparison.ctrl.vs.g11": 1 1 1 1 1 1 1 1 1 1 ...

  .. ..$ stim         : chr [1:3171] "CTRL" "CTRL" "CTRL" "CTRL" ...

  .. ..$ res.0.6      : chr [1:3171] "2" "4" "7" "0" ...

  .. ..$ celltype.stim: chr [1:3171] "c3_CTRL" "c5_CTRL" "c8_CTRL" "c1_CTRL" ...

  .. ..$ celltype     : chr [1:3171] "c3" "c5" "c8" "c1" ...

  ..@ project.name: chr "comparison.ctrl.vs.g11"

  ..@ dr          :List of 3

  .. ..$ cca        :Formal class 'dim.reduction' [package "Seurat"] with 7 slots

  .. .. .. ..@ cell.embeddings   : num [1:3171, 1:30] 0.0348 0.0264 0.0147 -0.0331 0.0375 ...

  .. .. .. .. ..- attr(*, "dimnames")=List of 2

  .. .. .. .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  .. .. .. .. .. ..$ : chr [1:30] "CC1" "CC2" "CC3" "CC4" ...

  .. .. .. ..@ gene.loadings     : num [1:1157, 1:30] 9.3 73.6 44.1 -23.2 -59.9 ...

  .. .. .. .. ..- attr(*, "dimnames")=List of 2

  .. .. .. .. .. ..$ : chr [1:1157] "Sprr1a" "S100a6" "Spp1" "Cartpt" ...

  .. .. .. .. .. ..$ : chr [1:30] "CC1" "CC2" "CC3" "CC4" ...

  .. .. .. ..@ gene.loadings.full: num [1:15213, 1:30] -2.73 -7.44 5.12 -9.41 -2.36 ...

  .. .. .. .. ..- attr(*, "dimnames")=List of 2

  .. .. .. .. .. ..$ : chr [1:15213] "Xkr4" "Rp1" "Mrpl15" "Lypla1" ...

  .. .. .. .. .. ..$ : chr [1:30] "CC1" "CC2" "CC3" "CC4" ...

  .. .. .. ..@ sdev              : num(0) 

  .. .. .. ..@ key               : chr "CC"

  .. .. .. ..@ jackstraw         : NULL

  .. .. .. ..@ misc              : NULL

  .. ..$ cca.aligned:Formal class 'dim.reduction' [package "Seurat"] with 7 slots

  .. .. .. ..@ cell.embeddings   : num [1:3171, 1:20] 1.421 1.058 0.551 -1.527 1.542 ...

  .. .. .. .. ..- attr(*, "dimnames")=List of 2

  .. .. .. .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  .. .. .. .. .. ..$ : chr [1:20] "ACC1" "ACC2" "ACC3" "ACC4" ...

  .. .. .. ..@ gene.loadings     : num[0 , 0 ] 

  .. .. .. ..@ gene.loadings.full: num[0 , 0 ] 

  .. .. .. ..@ sdev              : num(0) 

  .. .. .. ..@ key               : chr "ACC"

  .. .. .. ..@ jackstraw         : NULL

  .. .. .. ..@ misc              : NULL

  .. ..$ tsne       :Formal class 'dim.reduction' [package "Seurat"] with 7 slots

  .. .. .. ..@ cell.embeddings   : num [1:3171, 1:2] -33.16 -10.77 -5.71 26.2 -33.57 ...

  .. .. .. .. ..- attr(*, "dimnames")=List of 2

  .. .. .. .. .. ..$ : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  .. .. .. .. .. ..$ : chr [1:2] "tSNE_1" "tSNE_2"

  .. .. .. ..@ gene.loadings     : num[0 , 0 ] 

  .. .. .. ..@ gene.loadings.full: num[0 , 0 ] 

  .. .. .. ..@ sdev              : num(0) 

  .. .. .. ..@ key               : chr "tSNE_"

  .. .. .. ..@ jackstraw         : NULL

  .. .. .. ..@ misc              : NULL

  ..@ assay       : list()

  ..@ hvg.info    :'data.frame': 0 obs. of  0 variables

Formal class 'data.frame' [package "methods"] with 4 slots

  .. .. ..@ .Data    : list()

  .. .. ..@ names    : chr(0) 

  .. .. ..@ row.names: int(0) 

  .. .. ..@ .S3Class : chr "data.frame"

  ..@ imputed     :'data.frame': 0 obs. of  0 variables

Formal class 'data.frame' [package "methods"] with 4 slots

  .. .. ..@ .Data    : list()

  .. .. ..@ names    : chr(0) 

  .. .. ..@ row.names: int(0) 

  .. .. ..@ .S3Class : chr "data.frame"

  ..@ cell.names  : chr [1:3171] "ctrl_AAACCTGAGGATTCGG" "ctrl_AAACCTGAGTACTTGC" "ctrl_AAACCTGCAGATAATG" "ctrl_AAACGGGAGACGCACA" ...

  ..@ cluster.tree: list()

  ..@ snn         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots

  .. .. ..@ i       : int 0

  .. .. ..@ p       : int [1:2] 0 1

  .. .. ..@ Dim     : int [1:2] 1 1

  .. .. ..@ Dimnames:List of 2

  .. .. .. ..$ : NULL

  .. .. .. ..$ : NULL

  .. .. ..@ x       : num 1

  .. .. ..@ factors : list()

  ..@ calc.params :List of 7

  .. ..$ CreateSeuratObject  :List of 13

  .. .. ..$ project             : chr "comparison.ctrl.vs.g11"

  .. .. ..$ min.cells           : num 0

  .. .. ..$ min.genes           : num 0

  .. .. ..$ is.expr             : num 0

  .. .. ..$ normalization.method: NULL

  .. .. ..$ scale.factor        : num 10000

  .. .. ..$ do.scale            : logi FALSE

  .. .. ..$ do.center           : logi FALSE

  .. .. ..$ names.field         : num 1

  .. .. ..$ names.delim         : chr "_"

  .. .. ..$ display.progress    : logi TRUE

  .. .. ..$ ...                 : symbol 

  .. .. ..$ time                : POSIXct[1:1], format: "2019-01-05 18:33:46"

  .. ..$ NormalizeData       :List of 5

  .. .. ..$ assay.type          : chr "RNA"

  .. .. ..$ normalization.method: chr "LogNormalize"

  .. .. ..$ scale.factor        : num 10000

  .. .. ..$ display.progress    : logi TRUE

  .. .. ..$ time                : POSIXct[1:1], format: "2019-01-05 18:33:46"

  .. ..$ ScaleData           :List of 16

  .. .. ..$ genes.use         : chr [1:15213] "Xkr4" "Rp1" "Mrpl15" "Lypla1" ...

  .. .. ..$ vars.to.regress   : symbol 

  .. .. ..$ model.use         : chr "linear"

  .. .. ..$ use.umi           : logi FALSE

  .. .. ..$ do.scale          : logi TRUE

  .. .. ..$ do.center         : logi TRUE

  .. .. ..$ scale.max         : num 10

  .. .. ..$ block.size        : num 1000

  .. .. ..$ min.cells.to.block: num 3000

  .. .. ..$ display.progress  : logi TRUE

  .. .. ..$ assay.type        : chr "RNA"

  .. .. ..$ do.cpp            : logi TRUE

  .. .. ..$ check.for.norm    : logi TRUE

  .. .. ..$ do.par            : logi FALSE

  .. .. ..$ num.cores         : num 1

  .. .. ..$ time              : POSIXct[1:1], format: "2019-01-05 18:33:47"

  .. ..$ RunCCA              :List of 11

  .. .. ..$ group1         : symbol 

  .. .. ..$ group2         : symbol 

  .. .. ..$ group.by       : symbol 

  .. .. ..$ num.cc         : num 30

  .. .. ..$ genes.use      : chr [1:1157] "Sprr1a" "S100a6" "Spp1" "Cartpt" ...

  .. .. ..$ scale.data     : logi TRUE

  .. .. ..$ rescale.groups : logi FALSE

  .. .. ..$ ...            :length 2, mode "...": "ctrl" "stim"

  .. .. ..$ time           : POSIXct[1:1], format: "2019-01-05 18:33:53"

  .. .. ..$ object.project : chr "comparison.ctrl.vs.g11"

  .. .. ..$ object2.project: chr "comparison.ctrl.vs.g11"

  .. ..$ AlignSubspace.cca   :List of 9

  .. .. ..$ reduction.type    : chr "cca"

  .. .. ..$ grouping.var      : chr "stim"

  .. .. ..$ dims.align        : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...

  .. .. ..$ num.possible.genes: num 2000

  .. .. ..$ num.genes         : num 30

  .. .. ..$ show.plots        : logi FALSE

  .. .. ..$ verbose           : logi TRUE

  .. .. ..$ ...               : symbol 

  .. .. ..$ time              : POSIXct[1:1], format: "2019-01-05 18:35:41"

  .. ..$ RunTSNE             :List of 13

  .. .. ..$ reduction.use  : chr "cca.aligned"

  .. .. ..$ cells.use      : NULL

  .. .. ..$ dims.use       : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...

  .. .. ..$ genes.use      : NULL

  .. .. ..$ seed.use       : num 1

  .. .. ..$ tsne.method    : chr "Rtsne"

  .. .. ..$ add.iter       : num 0

  .. .. ..$ dim.embed      : num 2

  .. .. ..$ distance.matrix: NULL

  .. .. ..$ reduction.name : chr "tsne"

  .. .. ..$ reduction.key  : chr "tSNE_"

  .. .. ..$ ...            :length 1, mode "...": TRUE

  .. .. ..$ time           : POSIXct[1:1], format: "2019-01-05 18:37:25"

  .. ..$ FindClusters.res.0.6:List of 21

  .. .. ..$ genes.use         : NULL

  .. .. ..$ reduction.type    : chr "cca.aligned"

  .. .. ..$ dims.use          : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...

  .. .. ..$ k.param           : num 30

  .. .. ..$ plot.SNN          : logi FALSE

  .. .. ..$ prune.SNN         : num 0.0667

  .. .. ..$ print.output      : logi TRUE

  .. .. ..$ distance.matrix   : NULL

  .. .. ..$ save.SNN          : logi FALSE

  .. .. ..$ reuse.SNN         : logi FALSE

  .. .. ..$ force.recalc      : logi FALSE

  .. .. ..$ nn.eps            : num 0

  .. .. ..$ modularity.fxn    : num 1

  .. .. ..$ resolution        : num 0.6

  .. .. ..$ algorithm         : num 1

  .. .. ..$ n.start           : num 100

  .. .. ..$ n.iter            : num 10

  .. .. ..$ random.seed       : num 0

  .. .. ..$ temp.file.location: NULL

  .. .. ..$ edge.file.name    : NULL

  .. .. ..$ time              : POSIXct[1:1], format: "2019-01-05 18:37:25"

  ..@ kmeans      : NULL

  ..@ spatial     :Formal class 'spatial.info' [package "Seurat"] with 4 slots

  .. .. ..@ mix.probs    :'data.frame': 3171 obs. of  1 variable:

  .. .. .. ..$ nGene: int [1:3171] 1386 3798 1877 4852 1718 1882 2263 2217 1882 5222 ...

  .. .. ..@ mix.param    :'data.frame': 0 obs. of  0 variables

Formal class 'data.frame' [package "methods"] with 4 slots

  .. .. .. .. ..@ .Data    : list()

  .. .. .. .. ..@ names    : chr(0) 

  .. .. .. .. ..@ row.names: int(0) 

  .. .. .. .. ..@ .S3Class : chr "data.frame"

  .. .. ..@ final.prob   :'data.frame': 0 obs. of  0 variables

Formal class 'data.frame' [package "methods"] with 4 slots

  .. .. .. .. ..@ .Data    : list()

  .. .. .. .. ..@ names    : chr(0) 

  .. .. .. .. ..@ row.names: int(0) 

  .. .. .. .. ..@ .S3Class : chr "data.frame"

  .. .. ..@ insitu.matrix:'data.frame': 0 obs. of  0 variables

Formal class 'data.frame' [package "methods"] with 4 slots

  .. .. .. .. ..@ .Data    : list()

  .. .. .. .. ..@ names    : chr(0) 

  .. .. .. .. ..@ row.names: int(0) 

  .. .. .. .. ..@ .S3Class : chr "data.frame"

  ..@ misc        : NULL

  ..@ version     :Classes 'package_version', 'numeric_version'  hidden list of 1

  .. ..$ : int [1:3] 2 3 4
scRNA-seq seurat CCA • 372 views
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Entering edit mode
Aaron Lun ★ 27k
@alun
Last seen 11 hours ago
The city by the bay

As you well know, Seurat is not a Bioconductor package; you're better off asking the authors directly.

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