pipelineCNA: pipelineCNA Executes the entire SCEVAN pipeline that...
In AntonioDeFalco/SCEVAN: SCEVAN

pipelineCNA

R Documentation

pipelineCNA Executes the entire SCEVAN pipeline that classifies tumour and normal cells from the raw count matrix, infer the clonal profile of cancer cells and looks for possible sub-clones in the tumour cell matrix automatically analysing the specific and shared alterations of each subclone and a differential analysis of pathways and genes expressed in each subclone.

Description

pipelineCNA Executes the entire SCEVAN pipeline that classifies tumour and normal cells from the raw count matrix, infer the clonal profile of cancer cells and looks for possible sub-clones in the tumour cell matrix automatically analysing the specific and shared alterations of each subclone and a differential analysis of pathways and genes expressed in each subclone.

Usage

pipelineCNA(
  count_mtx,
  sample = "",
  par_cores = 20,
  norm_cell = NULL,
  SUBCLONES = TRUE,
  beta_vega = 0.5,
  ClonalCN = TRUE,
  plotTree = TRUE,
  AdditionalGeneSets = NULL,
  SCEVANsignatures = TRUE,
  organism = "human",
  ngenes_chr = 5,
  perc_genes = 10,
  FIXED_NORMAL_CELLS = FALSE
)

Arguments

`count_mtx`	Raw count matrix with genes on rows (both Gene Symbol or Ensembl ID are allowed) and cells on columns.
`sample`	Sample name to save results (optional)
`par_cores`	Number of cores to run the pipeline (optional - default 20)
`norm_cell`	Vector of possible known normal cells to be used as confident normal cells (optional)
`SUBCLONES`	Boolean value TRUE if you are interested in analysing the clonal structure and FALSE if you are only interested in the classification of malignant and non-malignant cells (optional - default TRUE)
`beta_vega`	Specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (optional - default 0.5)
`ClonalCN`	Get clonal CN profile inference from all tumour cells (optional)
`plotTree`	Plot Phylogenetic tree (optional - default FALSE)
`AdditionalGeneSets`	list of additional signatures of normal cell types (optional)
`SCEVANsignatures`	FALSE if you only want to use only the signatures specified in AdditionalGeneSets (default TRUE)
`organism`	Organism to be analysed (optional - "mouse" or "human" - default "human")
`ngenes_chr`	Minimum number of genes expressed on chromosome (optional - default 5)
`perc_genes`	Minimum percentage gene expressed in each cell (optional - default 10)
`FIXED_NORMAL_CELLS`	TRUE if norm_cell vector to be used as fixed reference, if you are only interested in clonal structure and not normal/tumor classification (default FALSE)