In matthieu-haudiquet/rothSGA: Rothstein Lab SGA Analysis Tools

SETUP

library(tidyverse)
library(rothSGA)
dir = params$dir
bio_rep_file            = file.path(dir, params$bio_rep_file)
processed_colonies_file = file.path(dir, params$processed_colonies_file)
processed_strains_file  = file.path(dir, params$processed_strains_file)

PLOTS GENERATED

plot_sm_data(params$processed_colonies_file, normalized = TRUE, path = params$dir)

QUALITY CONTROLS

Self-crossing queries (mixed library strain, wrong query, diploid escape)

rothSGA::check_self_crosses(params$dir)

Blank spots not blank (contamination, mispinning)

rothSGA::check_dead_strains(params$dir)

Sensitivity to the drug

rothSGA::check_query_sensitivity_to_drug(params$dir)

matthieu-haudiquet/rothSGA documentation built on May 14, 2019, 11:28 a.m.