config_case_control: setup configurations for this case control study

In brandonsie/phipcc: Generate Case-Control Reports from PhIP-seq Data

Description

writes table (defualt name config.tsv) with specified values. For input into define_plan_case_control()

Usage

config_case_control(filename = "config.tsv", proj_id, library, ctrl_id,
  delimiter, case_names, ctrl_names, input_dirs, data_types, data_names,
  data_level, min_hits_rcpgenerator, hit_thresh, rcp_thresh, stat_test,
  pval_correction, min_hits_enrichment, min_hits_rcp, min_freq_hits_rcp,
  pval_thresh, annot_path, peptide_col_id_match, protein_col_id_match,
  peptide_col_id_display, protein_col_id_display, description_col_id,
  flag_col_id, flag_type, pep_aa, binarize_clustergram,
  sample_field_delimiter, sample_key_field, run_epitopefindr, use_AVARDA,
  AVARDA_paths, AVARDA_seropos_grep, AVARDA_breadth_grep, remove_leading_x)

brandonsie/phipcc documentation built on June 2, 2020, 6:19 a.m.