wrap_ceres: CERES wrapper

In cancerdatasci/ceres: CERES for R

Description

CERES wrapper

Usage

wrap_ceres(sg_path, cn_path, guide_locus_path, locus_gene_path,
  replicate_map_path, run_id, optimize = F, params = NULL,
  cl_subset = NULL, fit_efficacy = T)

Arguments

sg_path	path to matrix with sgRNA sequences as row names, samples (i.e. replicates of cell line screens) as column names
cn_path	path to matrix with genomic cut sites as row names, cell lines as column names
guide_locus_path	path to data.frame with column names 'Guide' and 'Locus'. Values must match those corresponding to row names of sg_data and cn_data
locus_gene_path	path to data.frame with column names 'Locus' and 'Gene'
replicate_map_path	path to data.frame with column names 'Replicate' and 'CellLine'
run_id	name for the CERES run
optimize	toggle optimization routine
params	list of parameters; must specify or use defaults when optimize = F
fit_efficacy	boolean indicating whether sgRNA offsets and activity scores are computed

Value

A list of numeric vectors and matrices containing the results of the CERES fit.

cancerdatasci/ceres documentation built on May 20, 2019, 6:44 p.m.