README.md

In alex-kalinka-cruk/fgcMetadata: FGC CRISPR Metadata system

fgcMetadata

Summary

fgcMetadata is an R package containing functions to build an analysis config JSON file for use with the AZ-CRUK CRISPR pipeline. The package also saves csv files containing non-confidential metadata tables.

Installation

# install.packages("devtools")
devtools::install_github("TDLorg/fgcMetadata")

Usage

Build an analysis config object using pipes ('%>%'):

library(fgcMetadata)

# exp_file and samp_file: csv files from bench scientists.
# ci_submission_file: CI submission '.xlsx' file.
md <- start_fgc_project(data_dir = out_dir, 
                        project_id = "fgc_999", 
                        species = "human") %>%
  experiment_metadata(exp_file) %>%
  sample_metadata(samp_file) %>%
  sequencing_metadata(ci_submission_file) %>%
  add_analysis(name = "analysis-1",
               description = "Differential lethality") %>%
  add_plasmid(name = "plasmid_name",
              indices = NA,
              slx_id = "plasmid_name",
              counts_file = "plasmid_counts.txt") %>%
  # Comparisons:
  # (just one below, but any number can be added).
  add_comparison(name = "DiffLeth-Day7",
                 experiment = c("FGC_999_Parental","FGC_999_KnockOut"),
                 plasmid = "plasmid_name",
                 time_point_days = 7,
                 screen_goal = "sensitivity",
                 screen_type = "n",
                 library_annotation = "yusa_v3_human.1") %>%
  remove_unused_samples() %>%
  add_general(user_email = "[e-mail]") %>%
  add_meta()

Print a summary to the screen:

print(md)

Write an analysis config JSON file:

make_analysis_config_JSON(md, file = "config.JSON")

Bugs, Issues, Requests

Please contact Alex Kalinka

alex-kalinka-cruk/fgcMetadata documentation built on Oct. 29, 2020, 2:53 a.m.