We load the scRNA data of three samples MGH102 , MGH104 and MGH105 from the public dataset of Gliobastoma (GSE131928)
load(url("https://www.dropbox.com/s/esqvnltucdqajg1/listCountMtx.RData?raw=1"))
We run the pipeline that performs the classification of malignant and non-malignant cells of each sample and then the compare the inferred copy number between the different samples.
library(SCEVAN)
results <- SCEVAN::multiSampleComparisonClonalCN(listCountMtx, analysisName = "all", organism = "human" , par_cores = 20)
## [1] " raw data - genes: 23686 cells: 355"
## [1] "1) Filter: cells > 200 genes"
## [1] "2) Filter: genes > 10% of cells"
## [1] "12813 genes past filtering"
## [1] "3) Annotations gene coordinates"
## [1] "found 0 confident non malignant cells"
## [1] "11490 genes annotated"
## [1] "4) Filter: genes involved in the cell cycle"
## [1] "10928 genes past filtering "
## [1] "5) Filter: cells > 5genes per chromosome "
## [1] "6) Log Freeman Turkey transformation"
## [1] "A total of 355 cells, 10928 genes after preprocessing"
## [1] "7) Measuring baselines (pure tumor - synthetic normal cells)"
## [1] "8) Smoothing data"
## [1] "10) Adjust baseline"
## [1] "11) plot heatmap"
## [1] "found 355 tumor cells"
## [1] "time classify tumor cells: 35.0699315071106"
## [1] " raw data - genes: 23686 cells: 634"
## [1] "1) Filter: cells > 200 genes"
## [1] "2) Filter: genes > 10% of cells"
## [1] "12189 genes past filtering"
## [1] "3) Annotations gene coordinates"
## [1] "found 30 confident non malignant cells"
## [1] "10986 genes annotated"
## [1] "4) Filter: genes involved in the cell cycle"
## [1] "10481 genes past filtering "
## [1] "5) Filter: cells > 5genes per chromosome "
## [1] "6) Log Freeman Turkey transformation"
## [1] "A total of 634 cells, 10481 genes after preprocessing"
## [1] "7) Measuring baselines (confident normal cells)"
## [1] "8) Smoothing data"
## [1] "9) Segmentation (VegaMC)"
## [1] "10) Adjust baseline"
## [1] "11) plot heatmap"
## [1] "found 427 tumor cells"
## [1] "time classify tumor cells: 1.38624049425125"
## [1] " raw data - genes: 23686 cells: 312"
## [1] "1) Filter: cells > 200 genes"
## [1] "2) Filter: genes > 10% of cells"
## [1] "12359 genes past filtering"
## [1] "3) Annotations gene coordinates"
## [1] "found 30 confident non malignant cells"
## [1] "11153 genes annotated"
## [1] "4) Filter: genes involved in the cell cycle"
## [1] "10641 genes past filtering "
## [1] "5) Filter: cells > 5genes per chromosome "
## [1] "6) Log Freeman Turkey transformation"
## [1] "A total of 312 cells, 10641 genes after preprocessing"
## [1] "7) Measuring baselines (confident normal cells)"
## [1] "8) Smoothing data"
## [1] "9) Segmentation (VegaMC)"
## [1] "10) Adjust baseline"
## [1] "11) plot heatmap"
## [1] "found 216 tumor cells"
## [1] "time classify tumor cells: 49.321765422821"
The pipeline returns in results a data frame containing for each sample the classification (tumor/normal)
Copy Number of each sample.
OncoPrint-like plot that highlighting specific alteration, shared alteration between subclones, or clonal alteration.