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 = FALSE,
  plotTree = FALSE,
  AdditionalGeneSets = NULL,
  SCEVANsignatures = TRUE
)

Arguments

`count_mtx`	raw count matrix
`sample`	sample name (optional)
`par_cores`	number of cores (default 20)
`norm_cell`	vector of normal cells if already known (optional)
`SUBCLONES`	find subclones (default TRUE)
`beta_vega`	specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (default 0.5)
`ClonalCN`	clonal profile inference from tumour cells (optional)
`plotTree`	find subclones (optional)
`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)