prepare_ceres_inputs: CERES main routine

In cancerdatasci/ceres: CERES for R

Description

CERES main routine

Usage

prepare_ceres_inputs(inputs_dir, dep_file, pre_generated_guides_file = NULL,
  cn_seg_file, gene_annot_file, rep_map_file, genome_id = "hg19",
  chromosomes = paste0("chr", c(as.character(1:22), "X", "Y")),
  dep_normalize = "zmad", bowtie_exe = "bowtie",
  samtools_exe = "samtools", do_parallel = F, guide_alns_file = NULL)

Arguments

inputs_dir	directory path to write CERES inputs
dep_file	file path of guide-level dependency data. !!Not necessary if you have generate your guides with generate_guides
gene_annot_file	file path of gene annotation
guide_alns_file	Optional: file path of the guide mapped (use map_guide_to_locus to generate)
pre_generated_guides	Optional: Matrix generated by the generated_guides(dep_file) function. Will fasten this function (since we skip the reading of gct)
cn_seg	file path of segmented copy number data
rep_map	file path of replicate map

Value

Returns invisibly. Only called for its effects.

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