pipelineCNA: pipelineCNA Executes the entire SCEVAN pipeline that...

In AntonioDeFalco/SCEVAN: SCEVAN

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"
)

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 normal cells if the classification is already known and you are only interested in the clonal structure (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")

Examples

res_pip <- pipelineCNA(count_mtx)

AntonioDeFalco/SCEVAN documentation built on April 21, 2024, 7:52 p.m.