prepare_ceres_inputs: CERES main routine

Description Usage Arguments Value

Description

CERES main routine

Usage

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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.