sgains_pipeline: Integration with 'sGAINS' tool.

In seqpipe/SCclust: Clustering of Single Cell Sequencing Copy Number Profiles to Identify Clones

Description

This function is called by sGAINS tools to perform the final step in preparation of results: phylogenetic analysis of single-cell genomes represented by their copy-number profiles

Usage

sgains_pipeline(scgv_dir, case_name, varbin_dir, varbin_suffix,
  bins_boundaries_filename, cytoband, badbins = NULL, nsim = 150,
  sharemin = 0.85)

Arguments

scgv_dir	directory where the results of the analysis should be stored
case_name	name of the case to be used for storing results of the analysis
varbin_dir	directory where output of 'varbin' step of sGAINS (the binning scheme) is located
varbin_suffix	common suffix for files produced by 'varbin' step of sGAINS
cytoband	file name for a cytoband coordinate table for the version of the genome being used
badbins	a file name for a table of bad bins (bins with outlying read counts) for the specified binning scheme
nsim	number of simulations to run for calculating simulated FDR distribution
sharemin	a feature is considered 'widely shared' by leaves of a tree
bins_boundaries	file name for binning scheme to use in the analysis

seqpipe/SCclust documentation built on May 4, 2021, 11:56 a.m.