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.

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,
  output_dir = "./output"
)

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)

Examples

if (FALSE) { # \dontrun{
res_pip <- pipelineCNA(count_mtx)
} # }