Description Usage Arguments Value
CERES main routine
1 2 3 4 5 | 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)
|
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 |
Returns invisibly. Only called for its effects.
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